LRBA (LPS responsive beige-like anchor protein)

Gene

• Entrez ID: 987
• Gene name: LPS responsive beige-like anchor protein
• Gene symbol: LRBA
• Synonyms (NCBI Gene): BGL, CDC4L, CVID8, LAB300, LBA, uc.147
• Chromosome: 4
• Chromosome location: 4q31.3
• Summary: The protein encoded by this gene is a member of the WDL-BEACH-WD (WBW) gene family. Its expression is induced in B cells and macrophages by bacterial lipopolysaccharides (LPS). The encoded protein associates with protein kinase A and may be involved in le

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs17027133	T>C	Conflicting-interpretations-of-pathogenicity, benign	Genic upstream transcript variant, missense variant, coding sequence variant
rs62346982	T>G	Likely-benign, benign-likely-benign, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs79392371	T>C	Conflicting-interpretations-of-pathogenicity	Synonymous variant, genic upstream transcript variant, coding sequence variant
rs114610541	A>C	Conflicting-interpretations-of-pathogenicity, likely-benign	Missense variant, coding sequence variant, genic upstream transcript variant
rs116355217	T>C	Conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-benign	Missense variant, coding sequence variant, genic upstream transcript variant
rs138956153	C>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, genic upstream transcript variant, synonymous variant
rs140666848	T>C	Uncertain-significance, conflicting-interpretations-of-pathogenicity, benign-likely-benign	Missense variant, genic upstream transcript variant, coding sequence variant
rs142598024	C>G,T	Conflicting-interpretations-of-pathogenicity	Missense variant, genic upstream transcript variant, coding sequence variant
rs143625481	G>A,C	Conflicting-interpretations-of-pathogenicity	Missense variant, genic upstream transcript variant, coding sequence variant
rs145709687	G>A	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs145812385	G>A	Conflicting-interpretations-of-pathogenicity	Synonymous variant, genic upstream transcript variant, coding sequence variant
rs151286835	G>A,T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs199469662	G>A	Pathogenic	Coding sequence variant, genic upstream transcript variant, stop gained
rs199469663	A>C	Pathogenic	Coding sequence variant, missense variant
rs199469664	C>A,T	Pathogenic	Coding sequence variant, genic upstream transcript variant, stop gained, missense variant
rs200295901	A>G	Likely-pathogenic	Coding sequence variant, missense variant
rs201059532	T>C	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, genic upstream transcript variant, synonymous variant
rs727503779	CTCT>-,CT	Pathogenic	Frameshift variant, coding sequence variant
rs727503780	G>A,T	Pathogenic	Missense variant, stop gained, coding sequence variant, genic upstream transcript variant
rs745608560	C>G	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant, genic upstream transcript variant
rs762031957	G>C,T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, genic upstream transcript variant, synonymous variant
rs779575307	G>A,C	Pathogenic	Stop gained, coding sequence variant, genic upstream transcript variant, missense variant
rs1004337827	G>A	Likely-pathogenic	Coding sequence variant, stop gained
rs1171694504	C>A,T	Likely-pathogenic	Coding sequence variant, missense variant, stop gained
rs1181595292	A>T	Likely-pathogenic	Splice donor variant, genic upstream transcript variant
rs1192554889	G>C	Likely-pathogenic	Coding sequence variant, stop gained, genic upstream transcript variant
rs1206185362	G>A	Likely-pathogenic	Stop gained, coding sequence variant
rs1264504989	->CATG	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1484948342	G>A,C	Likely-pathogenic	Stop gained, coding sequence variant, missense variant, genic upstream transcript variant
rs1553956151	CAAG>-	Likely-pathogenic	Coding sequence variant, frameshift variant, genic upstream transcript variant
rs1553965868	AAGGAGAGGAG>-	Likely-pathogenic	Coding sequence variant, frameshift variant, genic upstream transcript variant
rs1553996145	A>C,G	Likely-pathogenic	Splice donor variant
rs1553998602	T>-	Likely-pathogenic	Coding sequence variant, frameshift variant, genic upstream transcript variant
rs1554020278	->TGTCTTCGCTAGC	Pathogenic	Stop gained, coding sequence variant, inframe indel, genic upstream transcript variant
rs1560914625	G>A	Pathogenic	Stop gained, coding sequence variant, genic upstream transcript variant
rs1560938296	TC>CA	Pathogenic	Stop gained, coding sequence variant, genic upstream transcript variant
rs1561254290	CT>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1578971328	G>A	Pathogenic	Genic upstream transcript variant, coding sequence variant, stop gained
rs1578999313	G>A	Likely-pathogenic	Genic upstream transcript variant, coding sequence variant, stop gained
rs1579059727	A>C	Likely-pathogenic	Genic upstream transcript variant, splice donor variant
rs1580875488	G>A	Pathogenic	Stop gained, coding sequence variant
rs1580974401	ATAGA>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1581303476	C>T	Pathogenic	Stop gained, coding sequence variant
rs1581401865	A>-	Pathogenic	Coding sequence variant, frameshift variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT040425	hsa-miR-615-3p	CLASH	23622248
MIRT039203	hsa-miR-769-5p	CLASH	23622248
MIRT038890	hsa-miR-93-3p	CLASH	23622248
MIRT036310	hsa-miR-1229-3p	CLASH	23622248
MIRT1117230	hsa-miR-1206	CLIP-seq
MIRT1117231	hsa-miR-1273d	CLIP-seq
MIRT1117232	hsa-miR-1322	CLIP-seq
MIRT1117233	hsa-miR-219-2-3p	CLIP-seq
MIRT1117234	hsa-miR-2355-5p	CLIP-seq
MIRT1117235	hsa-miR-2964a-3p	CLIP-seq
MIRT1117236	hsa-miR-33a	CLIP-seq
MIRT1117237	hsa-miR-33b	CLIP-seq
MIRT1117238	hsa-miR-3613-3p	CLIP-seq
MIRT1117239	hsa-miR-3647-3p	CLIP-seq
MIRT1117240	hsa-miR-3682-5p	CLIP-seq
MIRT1117241	hsa-miR-4286	CLIP-seq
MIRT1117242	hsa-miR-4652-3p	CLIP-seq
MIRT1117243	hsa-miR-4668-3p	CLIP-seq
MIRT1117244	hsa-miR-4680-3p	CLIP-seq
MIRT1117245	hsa-miR-4688	CLIP-seq
MIRT1117246	hsa-miR-4699-3p	CLIP-seq
MIRT1117247	hsa-miR-4793-5p	CLIP-seq
MIRT1117248	hsa-miR-486-3p	CLIP-seq
MIRT1117249	hsa-miR-767-3p	CLIP-seq
MIRT1117250	hsa-miR-1253	CLIP-seq
MIRT1117251	hsa-miR-1267	CLIP-seq
MIRT1117231	hsa-miR-1273d	CLIP-seq
MIRT1117252	hsa-miR-1273e	CLIP-seq
MIRT1117234	hsa-miR-2355-5p	CLIP-seq
MIRT1117253	hsa-miR-3065-3p	CLIP-seq
MIRT1117254	hsa-miR-3120-3p	CLIP-seq
MIRT1117255	hsa-miR-3121-3p	CLIP-seq
MIRT1117256	hsa-miR-3148	CLIP-seq
MIRT1117257	hsa-miR-3160-3p	CLIP-seq
MIRT1117258	hsa-miR-3185	CLIP-seq
MIRT1117259	hsa-miR-338-5p	CLIP-seq
MIRT1117239	hsa-miR-3647-3p	CLIP-seq
MIRT1117260	hsa-miR-3659	CLIP-seq
MIRT1117261	hsa-miR-3976	CLIP-seq
MIRT1117241	hsa-miR-4286	CLIP-seq
MIRT1117262	hsa-miR-4427	CLIP-seq
MIRT1117263	hsa-miR-4496	CLIP-seq
MIRT1117264	hsa-miR-4635	CLIP-seq
MIRT1117265	hsa-miR-4658	CLIP-seq
MIRT1117243	hsa-miR-4668-3p	CLIP-seq
MIRT1117266	hsa-miR-4684-3p	CLIP-seq
MIRT1117267	hsa-miR-4696	CLIP-seq
MIRT1117268	hsa-miR-4709-3p	CLIP-seq
MIRT1117269	hsa-miR-539	CLIP-seq
MIRT1117270	hsa-miR-574-5p	CLIP-seq
MIRT1117271	hsa-miR-628-5p	CLIP-seq
MIRT1117250	hsa-miR-1253	CLIP-seq
MIRT1117231	hsa-miR-1273d	CLIP-seq
MIRT1117256	hsa-miR-3148	CLIP-seq
MIRT1117257	hsa-miR-3160-3p	CLIP-seq
MIRT2033113	hsa-miR-323b-3p	CLIP-seq
MIRT2033114	hsa-miR-337-3p	CLIP-seq
MIRT1117260	hsa-miR-3659	CLIP-seq
MIRT2033115	hsa-miR-3685	CLIP-seq
MIRT2033116	hsa-miR-384	CLIP-seq
MIRT1117263	hsa-miR-4496	CLIP-seq
MIRT1117265	hsa-miR-4658	CLIP-seq
MIRT1117270	hsa-miR-574-5p	CLIP-seq
MIRT2263469	hsa-miR-1245b-5p	CLIP-seq
MIRT1117250	hsa-miR-1253	CLIP-seq
MIRT1117232	hsa-miR-1322	CLIP-seq
MIRT2263470	hsa-miR-198	CLIP-seq
MIRT2263471	hsa-miR-199a-3p	CLIP-seq
MIRT2263472	hsa-miR-199b-3p	CLIP-seq
MIRT2263473	hsa-miR-27a	CLIP-seq
MIRT2263474	hsa-miR-27b	CLIP-seq
MIRT1117253	hsa-miR-3065-3p	CLIP-seq
MIRT1117254	hsa-miR-3120-3p	CLIP-seq
MIRT2263475	hsa-miR-3123	CLIP-seq
MIRT2263476	hsa-miR-3129-5p	CLIP-seq
MIRT2263477	hsa-miR-3142	CLIP-seq
MIRT2263478	hsa-miR-3143	CLIP-seq
MIRT1117256	hsa-miR-3148	CLIP-seq
MIRT1117257	hsa-miR-3160-3p	CLIP-seq
MIRT2263479	hsa-miR-3174	CLIP-seq
MIRT2263480	hsa-miR-3529	CLIP-seq
MIRT1117260	hsa-miR-3659	CLIP-seq
MIRT2263481	hsa-miR-3671	CLIP-seq
MIRT1117240	hsa-miR-3682-5p	CLIP-seq
MIRT2263482	hsa-miR-3692	CLIP-seq
MIRT2263483	hsa-miR-371-5p	CLIP-seq
MIRT2263484	hsa-miR-371b-5p	CLIP-seq
MIRT2263485	hsa-miR-379	CLIP-seq
MIRT2263486	hsa-miR-4269	CLIP-seq
MIRT2263487	hsa-miR-4289	CLIP-seq
MIRT1117262	hsa-miR-4427	CLIP-seq
MIRT2263488	hsa-miR-4438	CLIP-seq
MIRT2263489	hsa-miR-4451	CLIP-seq
MIRT2263490	hsa-miR-4470	CLIP-seq
MIRT1117263	hsa-miR-4496	CLIP-seq
MIRT2263491	hsa-miR-4536	CLIP-seq
MIRT2263492	hsa-miR-4645-5p	CLIP-seq
MIRT2263493	hsa-miR-4650-3p	CLIP-seq
MIRT2263494	hsa-miR-4650-5p	CLIP-seq
MIRT1117265	hsa-miR-4658	CLIP-seq
MIRT2263495	hsa-miR-4673	CLIP-seq
MIRT2263496	hsa-miR-4742-5p	CLIP-seq
MIRT1117247	hsa-miR-4793-5p	CLIP-seq
MIRT2263497	hsa-miR-5095	CLIP-seq
MIRT2263498	hsa-miR-5096	CLIP-seq
MIRT2263499	hsa-miR-513a-5p	CLIP-seq
MIRT2263500	hsa-miR-513c	CLIP-seq
MIRT2263501	hsa-miR-514b-5p	CLIP-seq
MIRT2263502	hsa-miR-543	CLIP-seq
MIRT1117270	hsa-miR-574-5p	CLIP-seq
MIRT2263503	hsa-miR-576-3p	CLIP-seq
MIRT1117249	hsa-miR-767-3p	CLIP-seq
MIRT2263504	hsa-miR-921	CLIP-seq
MIRT1117250	hsa-miR-1253	CLIP-seq
MIRT1117256	hsa-miR-3148	CLIP-seq
MIRT1117257	hsa-miR-3160-3p	CLIP-seq
MIRT1117260	hsa-miR-3659	CLIP-seq
MIRT1117263	hsa-miR-4496	CLIP-seq
MIRT1117265	hsa-miR-4658	CLIP-seq
MIRT1117270	hsa-miR-574-5p	CLIP-seq
MIRT1117252	hsa-miR-1273e	CLIP-seq
MIRT1117264	hsa-miR-4635	CLIP-seq
MIRT1117252	hsa-miR-1273e	CLIP-seq
MIRT1117264	hsa-miR-4635	CLIP-seq

Transcription factors

Transcription factor	Regulation	Reference
E2F1	Activation	15064745

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000423	Process	Mitophagy	IMP	33773106
GO:0005515	Function	Protein binding	IPI	26206937, 31263572, 33961781
GO:0005764	Component	Lysosome	IEA
GO:0005765	Component	Lysosomal membrane	IEA
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005794	Component	Golgi apparatus	IDA
GO:0005794	Component	Golgi apparatus	IEA
GO:0005829	Component	Cytosol	IBA
GO:0005829	Component	Cytosol	IDA
GO:0005886	Component	Plasma membrane	IEA
GO:0008104	Process	Intracellular protein localization	IBA
GO:0016020	Component	Membrane	HDA	19946888
GO:0016020	Component	Membrane	IBA
GO:0016020	Component	Membrane	IEA
GO:0019901	Function	Protein kinase binding	IBA
GO:0034497	Process	Protein localization to phagophore assembly site	IMP	33773106

Other IDs

• MIM: 606453
• HGNC: 1742
• e!Ensembl: ENSG00000198589

Protein

• UniProt ID: P50851
• Protein name: Lipopolysaccharide-responsive and beige-like anchor protein (Beige-like protein) (CDC4-like protein)
• Protein function: Involved in coupling signal transduction and vesicle trafficking to enable polarized secretion and/or membrane deposition of immune effector molecules (By similarity). Involved in phagophore growth during mitophagy by regulating ATG9A traffickin
• PDB: 1T77
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF13385	Laminin_G_3	211 → 377		Domain
  PF15787	DUF4704	446 → 717	Domain of unknown function (DUF4704)	Family
  PF06469	DUF1088	1880 → 2058	Domain of Unknown Function (DUF1088)	Family
  PF14844	PH_BEACH	2084 → 2181	PH domain associated with Beige/BEACH	Domain
  PF02138	Beach	2213 → 2489	Beige/BEACH domain	Family

• Tissue specificity: TISSUE SPECIFICITY: Ubiquitous. {ECO:0000269|PubMed:12160729}.
• Sequence:

  MASEDNRVPSPPPTGDDGGGGGREETPTEGGALSLKPGLPIRGIRMKFAVLTGLVEVGEV
  SNRDIVETVFNLLVGGQFDLEMNFIIQEGESINCMVDLLEKCDITCQAEVWSMFTAILKK
  SIRNLQVCTEVGLVEKVLGKIEKVDNMIADLLVDMLGVLASYNLTVRELKLFFSKLQGDK
  GRWPPHAGKLLSVLKHMPQKYGPDAFFNFPGKSAAAIALPPIAKWPYQNGFTFHTWLRMD
  PVNNINVDKDKPYLYCFRTSKGLGYSAHFVGGCLIVTSIKSKGKGFQHCVKFDFKPQKWY
  MVTIVHIYNRWKNSELRCYVNGELASYGEITWFVNTSDTFDKCFLGSSETADANRVFCGQ
  MTAVYLFSEALNAAQIFAIYQLGLGYKGTFKFKAESDLFLAEHHKLLLYDGKLSSAIAFT
  YNPRATDAQLCLESSPKDNPSIFVHSPHALMLQDVKAVLTHSIQSAMHSIGGVQVLFPLF
  AQLDYRQYLSDEIDLTICSTLLAFIMELLKNSIAMQEQMLACKGFLVIGYSLEKSSKSHV
  SRAVLELCLAFSKYLSNLQNGMPLLKQLCDHVLLNPAIWIHTPAKVQLMLYTYLSTEFIG
  TVNIYNTIRRVGTVLLIMHTLKYYYWAVNPQDRSGITPKGLDGPRPNQKEMLSLRAFLLM
  FIKQLVMKDSGVKEDELQAILNYLLTMHEDDNLMDVLQLLVALMSEHPNSMIPAFDQRNG
  LRVIYKLLASKSEGIRVQALKAMGYFLKHLAPKRKAEVMLGHGLFSLLAERLMLQTNLIT
  MTTYNVLFEILIEQIGTQVIHKQHPDPDSSVKIQNPQILKVIATLLRNSPQCPESMEVRR
  AFLSDMIKLFNNSRENRRSLLQCSVWQEWMLSLCYFNPKNSDEQKITEMVYAIFRILLYH
  AVKYEWGGWRVWVDTLSITHSKVTFEIHKENLANIFREQQGKVDEEIGLCSSTSVQAASG
  IRRDINVSVGSQQPDTKDSPVCPHFTTNGNENSSIEKTSSLESASNIELQTTNTSYEEMK
  AEQENQELPDEGTLEETLTNETRNADDLEVSSDIIEAVAISSNSFITTGKDSMTVSEVTA
  SISSPSEEDASEMPEFLDKSIVEEEEDDDYVELKVEGSPTEEANLPTELQDNSLSPAASE
  AGEKLDMFGNDDKLIFQEGKPVTEKQTDTETQDSKDSGIQTMTASGSSAMSPETTVSQIA
  VESDLGQMLEEGKKATNLTRETKLINDCHGSVSEASSEQKIAKLDVSNVATDTERLELKA
  SPNVEAPQPHRHVLEISRQHEQPGQGIAPDAVNGQRRDSRSTVFRIPEFNWSQMHQRLLT
  DLLFSIETDIQMWRSHSTKTVMDFVNSSDNVIFVHNTIHLISQVMDNMVMACGGILPLLS
  AATSATHELENIEPTQGLSIEASVTFLQRLISLVDVLIFASSLGFTEIEAEKSMSSGGIL
  RQCLRLVCAVAVRNCLECQQHSQLKTRGDKALKPMHSLIPLGKSAAKSPVDIVTGGISPV
  RDLDRLLQDMDINRLRAVVFRDIEDSKQAQFLALAVVYFISVLMVSKYRDILEPQNERHS
  QSCTETGSENENVSLSEITPAAFSTLTTASVEESESTSSARRRDSGIGEETATGLGSHVE
  VTPHTAPPGVSAGPDAISEVLSTLSLEVNKSPETKNDRGNDLDTKATPSVSVSKNVNVKD
  ILRSLVNIPADGVTVDPALLPPACLGALGDLSVEQPVQFRSFDRSVIVAAKKSAVSPSTF
  NTSIPTNAVSVVSSVDSAQASDMGGESPGSRSSNAKLPSVPTVDSVSQDPVSNMSITERL
  EHALEKAAPLLREIFVDFAPFLSRTLLGSHGQELLIEGTSLVCMKSSSSVVELVMLLCSQ
  EWQNSIQKNAGLAFIELVNEGRLLSQTMKDHLVRVANEAEFILSRQRAEDIHRHAEFESL
  CAQYSADKREDEKMCDHLIRAAKYRDHVTATQLIQKIINILTDKHGAWGNSAVSRPLEFW
  RLDYWEDDLRRRRRFVRNPLGSTHPEATLKTAVEHVCIFKLRENSKATDEDILAKGKQSI
  RSQALGNQNSENEILLEGDDDTLSSVDEKDLENLAGPVSLSTPAQLVAPSVVVKGTLSVT
  SSELYFEVDEEDPNFKKIDPKILAYTEGLHGKWLFTEIRSIFSRRYLLQNTALEIFMANR
  VAVMFNFPDPATVKKVVNYLPRVGVGTSFGLPQTRRISLASPRQLFKASNMTQRWQHREI
  SNFEYLMFLNTIAGRSYNDLNQYPVFPWVITNYESEELDLTLPTNFRDLSKPIGALNPKR
  AAFFAERYESWEDDQVPKFHYGTHYSTASFVLAWLLRIEPFTTYFLNLQGGKFDHADRTF
  SSISRAWRNSQRDTSDIKELIPEFYYLPEMFVNFNNYNLGVMDDGTVVSDVELPPWAKTS
  EEFVHINRLALESEFVSCQLHQWIDLIFGYKQQGPEAVRALNVFYYLTYEGAVNLNSITD
  PVLREAVEAQIRSFGQTPSQLLIEPHPPRGSAMQVSPLMFTDKAQQDVIMVLKFPSNSPV
  THVAANTQPGLATPAVITVTANRLFAVNKWHNLPAHQGAVQDQPYQLPVEIDPLIASNTG
  MHRRQITDLLDQSIQVHSQCFVITSDNRYILVCGFWDKSFRVYSTDTGRLIQVVFGHWDV
  VTCLARSESYIGGNCYILSGSRDATLLLWYWNGKCSGIGDNPGSETAAPRAILTGHDYEV
  TCAAVCAELGLVLSGSQEGPCLIHSMNGDLLRTLEGPENCLKPKLIQASREGHCVIFYEN
  GLFCTFSVNGKLQATMETDDNIRAIQLSRDGQYLLTGGDRGVVVVRQVSDLKQLFAYPGC
  DAGIRAMALSYDQRCIISGMASGSIVLFYNDFNRWHHEYQTRY

• Sequence length: 2863

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Combined immunodeficiency due to LRBA deficiency	Likely pathogenic; Pathogenic	rs2126905499, rs2127009232, rs2151995373, rs760342862, rs2126810458, rs1319094744, rs1268711491, rs2126905382, rs2152104087, rs532289025, rs2149489382, rs1297757024, rs34237929, rs2149489346, rs2127154743, rs2127154885, rs1320366310, rs2126438478, rs2126810852, rs2149508349, rs2126988253, rs2126848251, rs1051619342, rs1032290659, rs777413769, rs2127004616, rs2149508258, rs1350061017, rs2546646309, rs727503779, rs727503780, rs2545994358, rs1209551499, rs2545893385, rs2546552538, rs2546501369, rs2547165271, rs1783240643, rs2546545150, rs2546559478, rs2545893731, rs2546423436, rs773780828, rs2546545055, rs748414191, rs1579044835, rs2546907359, rs2546693049, rs2546499925, rs1439160668, rs2546490347, rs746082628, rs2545740842, rs2546422057, rs2547368576, rs368167203, rs2547164192, rs1345661967, rs2546559508, rs2546547057, rs144451686, rs2547502929, rs2547502759, rs1323477178, rs2545728179, rs2546421991, rs746278403, rs1404249010, rs2546534919, rs2546545066, rs1170974293, rs747652653, rs1353022856, rs1192554889, rs779575307, rs199469663, rs199469662, rs199469664, rs1554020278, rs1560914625, rs755373718, rs1560938296, rs1484948342, rs1561254290, rs1580875488, rs1581303476, rs1181595292, rs1581401865, rs1264504989, rs1580974401, rs1206185362, rs1004337827, rs1578971328, rs1578999313, rs1750760771, rs745453685, rs1302362911, rs1730552437, rs1750701604, rs1750723817, rs1745202896, rs1772348297, rs764745197, rs1750245794, rs199750191, rs1729842757	RCV001594439 RCV001377647 RCV001385408 RCV001383085 RCV001381549 RCV001385766 RCV001873769 RCV001533553 RCV001782397 RCV003647015 RCV001809167 RCV001991632 RCV002037713 RCV001920949 RCV001970127 RCV001882063 RCV001953782 RCV001896457 RCV001943427 RCV001921351 RCV001921356 RCV002002462 RCV001871214 RCV001931945 RCV001958723 RCV002243596 RCV002251017 RCV002251118 RCV002283938 RCV000150103 RCV000150104 RCV003074620 RCV003084513 RCV002619319 RCV002636547 RCV002651853 RCV002731093 RCV002746292 RCV002843685 RCV002856399 RCV002862060 RCV002862061 RCV002851192 RCV002863693 RCV002963068 RCV003019959 RCV003024790 RCV003034927 RCV003036205 RCV003140544 RCV003142361 RCV003148570 RCV003152930 RCV003314374 RCV003314449 RCV003335929 RCV003337976 RCV003445291 RCV003448750 RCV003534025 RCV003531435 RCV003531737 RCV003531755 RCV003532384 RCV003532519 RCV003646419 RCV003646484 RCV003646703 RCV003646803 RCV003854040 RCV003852221 RCV004547362 RCV004577251 RCV005091139 RCV005010453 RCV000029134 RCV000029135 RCV000029136 RCV000650400 RCV000696141 RCV001244180 RCV000692077 RCV001594404 RCV000768379 RCV000803776 RCV000821001 RCV000818893 RCV000987478 RCV000991429 RCV000991430 RCV001041360 RCV001860584 RCV005012454 RCV001027974 RCV001071942 RCV001070004 RCV001065753 RCV001035308 RCV001207875 RCV001203869 RCV001229147 RCV001239515 RCV005012693 RCV002570417 RCV001267768 RCV001283807	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Inherited Immunodeficiency Diseases	Likely pathogenic; Pathogenic	rs1171694504, rs1578971328	RCV001027588 RCV001027587	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
LRBA-related disorder	Likely pathogenic	rs532289025, rs1425262198	RCV004750927 RCV003394377	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Severe combined immunodeficiency due to CORO1A deficiency	Pathogenic; Likely pathogenic	rs764745197, rs1750245794	RCV001250247 RCV001250246	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Benign; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ALZHEIMER DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BREAST CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BREAST CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHOLELITHIASIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Chronic lymphocytic leukemia/small lymphocytic lymphoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLOR VISION DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLORECTAL CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EBV-positive nodal T- and NK-cell lymphoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial pancreatic carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
FEMALE REPRODUCTIVE SYSTEM DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GALLSTONES	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hirschsprung disease, susceptibility to, 1	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Long QT syndrome	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lymphoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Meniere disease	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
MICROPHTHALMIA/COLOBOMA AND SKELETAL DYSPLASIA SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign; Likely benign; Uncertain significance; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PERIPHERAL ARTERIAL DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Spastic paraplegia, intellectual disability, nystagmus, and obesity	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Acquired Hypogammaglobulinemia	Common Variable Immunodeficiency	BEFREE	28956255		★☆☆☆☆ Found in Text Mining only
Agammaglobulinemia	Agammaglobulinemia	Pubtator	22608502, 30386343, 32284663, 35413226, 36074705	Associate	★☆☆☆☆ Found in Text Mining only
Anemia Hemolytic	Hemolytic anemia	Pubtator	35413226	Associate	★☆☆☆☆ Found in Text Mining only
Anemia Hemolytic Autoimmune	Autoimmune hemolytic anemia	Pubtator	35413226	Associate	★☆☆☆☆ Found in Text Mining only
Anthracosis	Anthracosis	BEFREE	28953250		★☆☆☆☆ Found in Text Mining only
Anthracosis	Anterior uveitis	Pubtator	28953250	Associate	★☆☆☆☆ Found in Text Mining only
Arthritis	Arthritis	BEFREE	28134088		★☆☆☆☆ Found in Text Mining only
Arthritis	Arthritis	Pubtator	36078750	Associate	★☆☆☆☆ Found in Text Mining only
Arthritis	Arthritis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Asthma	Asthma	BEFREE	30193889		★☆☆☆☆ Found in Text Mining only
Asthma	Asthma	HPO_DG			★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune disease	Pubtator	22608502, 28473463, 36078750	Associate	★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune Diseases	BEFREE	26206937, 26707784, 27057999, 28134088, 28197149, 28601686, 28652580, 28720148, 28806575, 30107266, 30995531, 31389321		★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases of the Nervous System	Autoimmune nervous system disorder	Pubtator	36790564	Associate	★☆☆☆☆ Found in Text Mining only
Autoimmune hemolytic anemia	Autoimmune hemolytic anemia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Autoimmune Lymphoproliferative Syndrome	Autoimmune lymphoproliferative disorder	Pubtator	28473463	Associate	★☆☆☆☆ Found in Text Mining only
Autoimmune Lymphoproliferative Syndrome	Autoimmune Lymphoproliferative Disorder	BEFREE	31432443		★☆☆☆☆ Found in Text Mining only
Bohring syndrome	Bohring syndrome	Pubtator	35413226	Associate	★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	23819905	Associate	★☆☆☆☆ Found in Text Mining only
Bronchiectasis	Bronchiectasis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Carcinoma in situ of uterine cervix	Cervical Intraepithelial Neoplasia	BEFREE	20615884		★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	25468195	Associate	★☆☆☆☆ Found in Text Mining only
Cervical Intraepithelial Neoplasia	Cervical Intraepithelial Neoplasia	BEFREE	18461626		★☆☆☆☆ Found in Text Mining only
Chronic granulomatous disease	Granulomatous Disease	BEFREE	27873163, 28684198		★☆☆☆☆ Found in Text Mining only
Chronic lung disease	Lung Diseases	HPO_DG			★☆☆☆☆ Found in Text Mining only
Colitis	Colitis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Combined immunodeficiency	Severe combined immunodeficiency disease	BEFREE	22721650, 25931386, 28512785, 31389321		★☆☆☆☆ Found in Text Mining only
Combined immunodeficiency due to LRBA deficiency	Immunodeficiency	Orphanet			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Common Variable Immunodeficiency	Common variable immunodeficiency	Pubtator	26122175, 27016798, 27888588, 29867916, 30363934, 32154999, 33912197, 36074705, 40703516	Associate	★☆☆☆☆ Found in Text Mining only
Common Variable Immunodeficiency	Common Variable Immunodeficiency	BEFREE	27146671, 28134088, 28956255, 30193889, 31432443		★☆☆☆☆ Found in Text Mining only
Conjunctivitis	Conjunctivitis	HPO_DG			★☆☆☆☆ Found in Text Mining only
CTLA4 deficiency	CTLA4 Deficiency	BEFREE	28601686, 28806575, 30107266		★☆☆☆☆ Found in Text Mining only
CTLA4 Haploinsufficiency	CTLA4 deficiency	BEFREE	27873163, 31156616		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes mellitus	Pubtator	28473463, 29417186, 36078750, 36423945, 38408297	Associate	★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus Congenital Autoimmune	Diabetes mellitus	Pubtator	38408297	Associate	★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus Transient Neonatal 1	Diabetes mellitus transient neonatal	Pubtator	28473463, 33845048, 36423945	Associate	★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus Type 1	Diabetes mellitus, type 1	Pubtator	33845048, 33912197, 36078750	Associate	★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Insulin-Dependent	Diabetes Mellitus	BEFREE	27057999		★☆☆☆☆ Found in Text Mining only
Diabetic Retinopathy	Diabetic retinopathy	Pubtator	39924156	Associate	★☆☆☆☆ Found in Text Mining only
Diarrhea	Diarrhea	Pubtator	33013830, 36078750	Associate	★☆☆☆☆ Found in Text Mining only
Evans syndrome	Evans Syndrome	BEFREE	29330115, 30188351		★☆☆☆☆ Found in Text Mining only
Gastric Adenocarcinoma	Gastric Cancer	BEFREE	28720148		★☆☆☆☆ Found in Text Mining only
Gastritis	Gastritis	Pubtator	33717114	Associate	★☆☆☆☆ Found in Text Mining only
Gastritis	Gastritis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hematologic Diseases	Hematologic disease	Pubtator	31874111, 36074705	Associate	★☆☆☆☆ Found in Text Mining only
Hemolysis	Hemolysis	Pubtator	35413226	Associate	★☆☆☆☆ Found in Text Mining only
Hyperglycemia	Hyperglycemia	BEFREE	27339152		★☆☆☆☆ Found in Text Mining only
Hypogammaglobulinemia	Hypogammaglobulinemia	BEFREE	26768763, 27146671, 28512785, 30386343, 31486986		★☆☆☆☆ Found in Text Mining only
Hypoglycemia	Hypoglycemia	BEFREE	28438244		★☆☆☆☆ Found in Text Mining only
Hypoglycemia	Hypoglycemia	Pubtator	36078750	Associate	★☆☆☆☆ Found in Text Mining only
Hypothyroidism	Hypothyroidism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Immune System Diseases	Immune system disease	Pubtator	22608502, 32592188, 35413226, 35482138, 36074705	Associate	★☆☆☆☆ Found in Text Mining only
Immune System Diseases	Immune System Diseases	BEFREE	26206937		★☆☆☆☆ Found in Text Mining only
IMMUNODEFICIENCY, COMMON VARIABLE, 8, WITH AUTOIMMUNITY	Common variable immunodeficiency	ORPHANET_DG	22608502, 25468195		★☆☆☆☆ Found in Text Mining only
IMMUNODEFICIENCY, COMMON VARIABLE, 8, WITH AUTOIMMUNITY	Common variable immunodeficiency	GENOMICS_ENGLAND_DG	22608502, 22721650, 25479458, 27057999, 27302973, 28473463		★☆☆☆☆ Found in Text Mining only
IMMUNODEFICIENCY, COMMON VARIABLE, 8, WITH AUTOIMMUNITY	Common variable immunodeficiency	UNIPROT_DG	22608502		★☆☆☆☆ Found in Text Mining only
IMMUNODEFICIENCY, COMMON VARIABLE, 8, WITH AUTOIMMUNITY	Common variable immunodeficiency	CLINVAR_DG	28473463		★☆☆☆☆ Found in Text Mining only
IMMUNODEFICIENCY, COMMON VARIABLE, 8, WITH AUTOIMMUNITY	Common variable immunodeficiency	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Immunologic Deficiency Syndromes	Immunologic Deficiency Syndromes	BEFREE	26206937, 27057999, 28197149, 28690850, 30188351		★☆☆☆☆ Found in Text Mining only
Immunologic Deficiency Syndromes	Immunologic Deficiency Syndromes	HPO_DG			★☆☆☆☆ Found in Text Mining only
Inflammatory Bowel Diseases	Inflammatory Bowel Disease	BEFREE	22721650, 28551707, 28956255, 30188351, 30714845		★☆☆☆☆ Found in Text Mining only
Inflammatory Bowel Diseases	Inflammatory bowel disease	Pubtator	22721650, 27888588, 32084423, 33013830, 33359885, 35413226	Associate	★☆☆☆☆ Found in Text Mining only
Intestinal Diseases	Intestinal Diseases	BEFREE	27146671, 28512785		★☆☆☆☆ Found in Text Mining only
Juvenile arthritis	Arthritis	BEFREE	28134088		★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	GWASCAT_DG	27903959		★☆☆☆☆ Found in Text Mining only
Lymphohistiocytosis Hemophagocytic	Hemophagocytic lymphohistiocytosis	Pubtator	36074705	Associate	★☆☆☆☆ Found in Text Mining only
Lymphoproliferative Disorders	Lymphoproliferative syndrome	Pubtator	36074705	Associate	★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	UNIPROT_DG			★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	28720148		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	15064745, 28720148		★☆☆☆☆ Found in Text Mining only
melanoma	Melanoma	BEFREE	28720148		★☆☆☆☆ Found in Text Mining only
Melanoma	Melanoma	Pubtator	28720148	Associate	★☆☆☆☆ Found in Text Mining only
Metabolic Diseases	Metabolic syndrome	Pubtator	25468195	Associate	★☆☆☆☆ Found in Text Mining only
MICROPHTHALMIA/COLOBOMA AND SKELETAL DYSPLASIA SYNDROME	MICROPHTHALMIA/COLOBOMA AND SKELETAL DYSPLASIA SYNDROME	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Migraine without Aura	Migraine	Pubtator	28473463	Associate	★☆☆☆☆ Found in Text Mining only
Mild cognitive disorder	Cognitive disorder	BEFREE	31698011		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	15064745		★☆☆☆☆ Found in Text Mining only
Neutropenia	Neutropenia	Pubtator	33912197	Associate	★☆☆☆☆ Found in Text Mining only
Panniculitis	Panniculitis	Pubtator	31874111	Associate	★☆☆☆☆ Found in Text Mining only
Periodontitis	Periodontitis	BEFREE	29672992		★☆☆☆☆ Found in Text Mining only
Polyarthritis	Polyarthritis	BEFREE	27057999		★☆☆☆☆ Found in Text Mining only
Pulmonary Fibrosis	Pulmonary fibrosis	Pubtator	28953250	Associate	★☆☆☆☆ Found in Text Mining only
Recurrent otitis media	Otitis media	HPO_DG			★☆☆☆☆ Found in Text Mining only
Recurrent sinusitis	Sinusitis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	28720148		★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	28720148	Associate	★☆☆☆☆ Found in Text Mining only
Van der Woude syndrome	Van der woude syndrome	Pubtator	27888588, 32284663, 36074705	Inhibit	★☆☆☆☆ Found in Text Mining only
Van der Woude syndrome	Van der woude syndrome	Pubtator	27888588, 35413226	Associate	★☆☆☆☆ Found in Text Mining only