SETD1A (SET domain containing 1A, histone lysine methyltransferase)

Gene

• Entrez ID: 9739
• Gene name: SET domain containing 1A, histone lysine methyltransferase
• Gene symbol: SETD1A
• Synonyms (NCBI Gene): EPEDD, EPEO2, KMT2F, NEDSID, Set1, Set1A
• Chromosome: 16
• Chromosome location: 16p11.2
• Summary: The protein encoded by this gene is a component of a histone methyltransferase (HMT) complex that produces mono-, di-, and trimethylated histone H3 at Lys4. Trimethylation of histone H3 at lysine 4 (H3K4me3) is a chromatin modification known to generally

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs770913157	C>G,T	Pathogenic	Coding sequence variant, stop gained, synonymous variant
rs869312829	A>G	Pathogenic	Splice acceptor variant
rs869312830	C>-	Pathogenic	Frameshift variant, coding sequence variant
rs869312831	C>T	Pathogenic	Stop gained, coding sequence variant
rs869312832	->C	Pathogenic	Frameshift variant, coding sequence variant
rs1555488653	A>-	Pathogenic	Frameshift variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT051709	hsa-let-7e-5p	CLASH	23622248
MIRT044797	hsa-miR-320a	CLASH	23622248
MIRT044067	hsa-miR-361-5p	CLASH	23622248
MIRT040819	hsa-miR-18a-3p	CLASH	23622248
MIRT036712	hsa-miR-760	CLASH	23622248
MIRT711595	hsa-miR-5003-3p	HITS-CLIP	19536157
MIRT711594	hsa-miR-6892-3p	HITS-CLIP	19536157
MIRT711593	hsa-miR-2276-5p	HITS-CLIP	19536157
MIRT711592	hsa-miR-3183	HITS-CLIP	19536157
MIRT711591	hsa-miR-4723-3p	HITS-CLIP	19536157
MIRT711590	hsa-miR-6769b-3p	HITS-CLIP	19536157
MIRT711589	hsa-miR-6515-3p	HITS-CLIP	19536157
MIRT711588	hsa-miR-1236-3p	HITS-CLIP	19536157
MIRT711587	hsa-miR-676-5p	HITS-CLIP	19536157
MIRT711586	hsa-miR-642a-5p	HITS-CLIP	19536157
MIRT711585	hsa-miR-4755-5p	HITS-CLIP	19536157
MIRT711583	hsa-miR-5006-3p	HITS-CLIP	19536157
MIRT711584	hsa-miR-4446-5p	HITS-CLIP	19536157
MIRT696118	hsa-miR-548av-3p	HITS-CLIP	23313552
MIRT696117	hsa-miR-548g-3p	HITS-CLIP	23313552
MIRT696116	hsa-miR-942-3p	HITS-CLIP	23313552
MIRT696115	hsa-miR-5195-5p	HITS-CLIP	23313552
MIRT696114	hsa-miR-4716-3p	HITS-CLIP	23313552
MIRT696113	hsa-miR-6794-5p	HITS-CLIP	23313552
MIRT696112	hsa-miR-6890-3p	HITS-CLIP	23313552
MIRT696111	hsa-miR-6798-5p	HITS-CLIP	23313552
MIRT696110	hsa-miR-1273g-3p	HITS-CLIP	23313552
MIRT696109	hsa-miR-1915-3p	HITS-CLIP	23313552
MIRT696108	hsa-miR-6764-5p	HITS-CLIP	23313552
MIRT696107	hsa-miR-1913	HITS-CLIP	23313552
MIRT696106	hsa-miR-324-3p	HITS-CLIP	23313552
MIRT696105	hsa-miR-6846-3p	HITS-CLIP	23313552
MIRT696104	hsa-miR-4252	HITS-CLIP	23313552
MIRT696103	hsa-miR-5699-5p	HITS-CLIP	23313552
MIRT696102	hsa-miR-4758-3p	HITS-CLIP	23313552
MIRT696101	hsa-miR-3189-5p	HITS-CLIP	23313552
MIRT696100	hsa-miR-6878-5p	HITS-CLIP	23313552
MIRT696099	hsa-miR-3175	HITS-CLIP	23313552
MIRT696098	hsa-miR-4723-5p	HITS-CLIP	23313552
MIRT696097	hsa-miR-5698	HITS-CLIP	23313552
MIRT696096	hsa-miR-6870-5p	HITS-CLIP	23313552
MIRT696095	hsa-miR-7111-5p	HITS-CLIP	23313552
MIRT696094	hsa-miR-4701-5p	HITS-CLIP	23313552
MIRT696093	hsa-miR-588	HITS-CLIP	23313552
MIRT711595	hsa-miR-5003-3p	HITS-CLIP	19536157
MIRT711594	hsa-miR-6892-3p	HITS-CLIP	19536157
MIRT711593	hsa-miR-2276-5p	HITS-CLIP	19536157
MIRT711592	hsa-miR-3183	HITS-CLIP	19536157
MIRT711591	hsa-miR-4723-3p	HITS-CLIP	19536157
MIRT711590	hsa-miR-6769b-3p	HITS-CLIP	19536157
MIRT711589	hsa-miR-6515-3p	HITS-CLIP	19536157
MIRT711588	hsa-miR-1236-3p	HITS-CLIP	19536157
MIRT711587	hsa-miR-676-5p	HITS-CLIP	19536157
MIRT711586	hsa-miR-642a-5p	HITS-CLIP	19536157
MIRT711585	hsa-miR-4755-5p	HITS-CLIP	19536157
MIRT711583	hsa-miR-5006-3p	HITS-CLIP	19536157
MIRT711584	hsa-miR-4446-5p	HITS-CLIP	19536157
MIRT696118	hsa-miR-548av-3p	HITS-CLIP	23313552
MIRT696117	hsa-miR-548g-3p	HITS-CLIP	23313552
MIRT696116	hsa-miR-942-3p	HITS-CLIP	23313552
MIRT696115	hsa-miR-5195-5p	HITS-CLIP	23313552
MIRT696114	hsa-miR-4716-3p	HITS-CLIP	23313552
MIRT696113	hsa-miR-6794-5p	HITS-CLIP	23313552
MIRT696112	hsa-miR-6890-3p	HITS-CLIP	23313552
MIRT696111	hsa-miR-6798-5p	HITS-CLIP	23313552
MIRT696110	hsa-miR-1273g-3p	HITS-CLIP	23313552
MIRT696109	hsa-miR-1915-3p	HITS-CLIP	23313552
MIRT696108	hsa-miR-6764-5p	HITS-CLIP	23313552
MIRT696107	hsa-miR-1913	HITS-CLIP	23313552
MIRT696106	hsa-miR-324-3p	HITS-CLIP	23313552
MIRT696105	hsa-miR-6846-3p	HITS-CLIP	23313552
MIRT696104	hsa-miR-4252	HITS-CLIP	23313552
MIRT696103	hsa-miR-5699-5p	HITS-CLIP	23313552
MIRT696102	hsa-miR-4758-3p	HITS-CLIP	23313552
MIRT696101	hsa-miR-3189-5p	HITS-CLIP	23313552
MIRT696100	hsa-miR-6878-5p	HITS-CLIP	23313552
MIRT696099	hsa-miR-3175	HITS-CLIP	23313552
MIRT696098	hsa-miR-4723-5p	HITS-CLIP	23313552
MIRT696097	hsa-miR-5698	HITS-CLIP	23313552
MIRT696096	hsa-miR-6870-5p	HITS-CLIP	23313552
MIRT696095	hsa-miR-7111-5p	HITS-CLIP	23313552
MIRT696094	hsa-miR-4701-5p	HITS-CLIP	23313552
MIRT696093	hsa-miR-588	HITS-CLIP	23313552
MIRT1339799	hsa-miR-1207-5p	CLIP-seq
MIRT1339800	hsa-miR-1225-3p	CLIP-seq
MIRT1339801	hsa-miR-1233	CLIP-seq
MIRT1339802	hsa-miR-1283	CLIP-seq
MIRT1339803	hsa-miR-1291	CLIP-seq
MIRT1339804	hsa-miR-1293	CLIP-seq
MIRT1339805	hsa-miR-1909	CLIP-seq
MIRT1339806	hsa-miR-221	CLIP-seq
MIRT1339807	hsa-miR-222	CLIP-seq
MIRT1339808	hsa-miR-296-5p	CLIP-seq
MIRT1339809	hsa-miR-299-3p	CLIP-seq
MIRT1339810	hsa-miR-3064-5p	CLIP-seq
MIRT1339811	hsa-miR-3121-3p	CLIP-seq
MIRT1339812	hsa-miR-3143	CLIP-seq
MIRT1339813	hsa-miR-3173-5p	CLIP-seq
MIRT1339814	hsa-miR-3692	CLIP-seq
MIRT1339815	hsa-miR-370	CLIP-seq
MIRT1339816	hsa-miR-378g	CLIP-seq
MIRT1339817	hsa-miR-4258	CLIP-seq
MIRT1339818	hsa-miR-4260	CLIP-seq
MIRT1339819	hsa-miR-4261	CLIP-seq
MIRT1339820	hsa-miR-4265	CLIP-seq
MIRT1339821	hsa-miR-4296	CLIP-seq
MIRT1339822	hsa-miR-4301	CLIP-seq
MIRT1339823	hsa-miR-4322	CLIP-seq
MIRT1339824	hsa-miR-4417	CLIP-seq
MIRT1339825	hsa-miR-4455	CLIP-seq
MIRT1339826	hsa-miR-4475	CLIP-seq
MIRT1339827	hsa-miR-4483	CLIP-seq
MIRT1339828	hsa-miR-4496	CLIP-seq
MIRT1339829	hsa-miR-455-3p	CLIP-seq
MIRT1339830	hsa-miR-4651	CLIP-seq
MIRT1339831	hsa-miR-4663	CLIP-seq
MIRT1339832	hsa-miR-4690-3p	CLIP-seq
MIRT1339833	hsa-miR-4726-3p	CLIP-seq
MIRT1339834	hsa-miR-4763-3p	CLIP-seq
MIRT1339835	hsa-miR-4803	CLIP-seq
MIRT1339836	hsa-miR-541	CLIP-seq
MIRT1339837	hsa-miR-545	CLIP-seq
MIRT1339838	hsa-miR-548p	CLIP-seq
MIRT1339839	hsa-miR-548v	CLIP-seq
MIRT1339840	hsa-miR-604	CLIP-seq
MIRT1339841	hsa-miR-608	CLIP-seq
MIRT1339842	hsa-miR-625	CLIP-seq
MIRT1339843	hsa-miR-647	CLIP-seq
MIRT1339844	hsa-miR-654-5p	CLIP-seq
MIRT1339845	hsa-miR-711	CLIP-seq
MIRT1339799	hsa-miR-1207-5p	CLIP-seq
MIRT2100459	hsa-miR-142-5p	CLIP-seq
MIRT2100460	hsa-miR-1827	CLIP-seq
MIRT1339805	hsa-miR-1909	CLIP-seq
MIRT2100461	hsa-miR-22	CLIP-seq
MIRT1339808	hsa-miR-296-5p	CLIP-seq
MIRT2100462	hsa-miR-298	CLIP-seq
MIRT1339812	hsa-miR-3143	CLIP-seq
MIRT2100463	hsa-miR-3163	CLIP-seq
MIRT2100464	hsa-miR-340	CLIP-seq
MIRT2100465	hsa-miR-34b	CLIP-seq
MIRT1339814	hsa-miR-3692	CLIP-seq
MIRT1339816	hsa-miR-378g	CLIP-seq
MIRT1339818	hsa-miR-4260	CLIP-seq
MIRT1339819	hsa-miR-4261	CLIP-seq
MIRT2100466	hsa-miR-4438	CLIP-seq
MIRT1339828	hsa-miR-4496	CLIP-seq
MIRT1339829	hsa-miR-455-3p	CLIP-seq
MIRT1339832	hsa-miR-4690-3p	CLIP-seq
MIRT1339833	hsa-miR-4726-3p	CLIP-seq
MIRT1339834	hsa-miR-4763-3p	CLIP-seq
MIRT2100467	hsa-miR-4768-3p	CLIP-seq
MIRT1339835	hsa-miR-4803	CLIP-seq
MIRT2100468	hsa-miR-5095	CLIP-seq
MIRT1339836	hsa-miR-541	CLIP-seq
MIRT2100469	hsa-miR-542-3p	CLIP-seq
MIRT1339837	hsa-miR-545	CLIP-seq
MIRT2100470	hsa-miR-548c-3p	CLIP-seq
MIRT1339838	hsa-miR-548p	CLIP-seq
MIRT2100471	hsa-miR-561	CLIP-seq
MIRT1339844	hsa-miR-654-5p	CLIP-seq
MIRT2100472	hsa-miR-720	CLIP-seq
MIRT1339799	hsa-miR-1207-5p	CLIP-seq
MIRT1339808	hsa-miR-296-5p	CLIP-seq
MIRT2100463	hsa-miR-3163	CLIP-seq
MIRT2100464	hsa-miR-340	CLIP-seq
MIRT2100465	hsa-miR-34b	CLIP-seq
MIRT1339816	hsa-miR-378g	CLIP-seq
MIRT1339818	hsa-miR-4260	CLIP-seq
MIRT1339834	hsa-miR-4763-3p	CLIP-seq
MIRT2100470	hsa-miR-548c-3p	CLIP-seq
MIRT2100472	hsa-miR-720	CLIP-seq
MIRT2620871	hsa-miR-1182	CLIP-seq
MIRT1339799	hsa-miR-1207-5p	CLIP-seq
MIRT2620872	hsa-miR-1245b-3p	CLIP-seq
MIRT2620873	hsa-miR-1266	CLIP-seq
MIRT2100460	hsa-miR-1827	CLIP-seq
MIRT2620874	hsa-miR-3128	CLIP-seq
MIRT2620875	hsa-miR-3190	CLIP-seq
MIRT2620876	hsa-miR-3202	CLIP-seq
MIRT2620877	hsa-miR-4518	CLIP-seq
MIRT2620878	hsa-miR-4533	CLIP-seq
MIRT2620879	hsa-miR-4720-5p	CLIP-seq
MIRT2620880	hsa-miR-4725-5p	CLIP-seq
MIRT2620881	hsa-miR-4733-3p	CLIP-seq
MIRT2620882	hsa-miR-4736	CLIP-seq
MIRT1339834	hsa-miR-4763-3p	CLIP-seq
MIRT2620883	hsa-miR-4799-3p	CLIP-seq
MIRT2620884	hsa-miR-504	CLIP-seq
MIRT2620885	hsa-miR-873	CLIP-seq
MIRT2620886	hsa-miR-940	CLIP-seq
MIRT2620871	hsa-miR-1182	CLIP-seq
MIRT1339799	hsa-miR-1207-5p	CLIP-seq
MIRT2620873	hsa-miR-1266	CLIP-seq
MIRT2620875	hsa-miR-3190	CLIP-seq
MIRT2620876	hsa-miR-3202	CLIP-seq
MIRT2620877	hsa-miR-4518	CLIP-seq
MIRT2620878	hsa-miR-4533	CLIP-seq
MIRT2620880	hsa-miR-4725-5p	CLIP-seq
MIRT2620881	hsa-miR-4733-3p	CLIP-seq
MIRT1339834	hsa-miR-4763-3p	CLIP-seq
MIRT2620884	hsa-miR-504	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	IDA	27141965
GO:0003676	Function	Nucleic acid binding	IEA
GO:0003723	Function	RNA binding	IDA	38003223
GO:0003723	Function	RNA binding	IEA
GO:0005515	Function	Protein binding	IPI	12670868, 17998332, 18765639, 20622854, 22266653, 22665483, 22723415, 22843687, 23870121, 26886794, 33961781, 37030068
GO:0005634	Component	Nucleus	IDA	17500065
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	IMP	22723415
GO:0005654	Component	Nucleoplasm	TAS
GO:0005694	Component	Chromosome	IEA
GO:0005737	Component	Cytoplasm	IDA	38003223
GO:0005737	Component	Cytoplasm	IEA
GO:0006325	Process	Chromatin organization	IEA
GO:0006338	Process	Chromatin remodeling	IEA
GO:0006974	Process	DNA damage response	IEA
GO:0007420	Process	Brain development	IMP	31197650
GO:0008013	Function	Beta-catenin binding	IPI	22723415
GO:0008168	Function	Methyltransferase activity	IEA
GO:0016607	Component	Nuclear speck	IDA	38003223
GO:0016607	Component	Nuclear speck	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0032259	Process	Methylation	IEA
GO:0035097	Component	Histone methyltransferase complex	IDA	17355966, 17500065
GO:0042800	Function	Histone H3K4 methyltransferase activity	IBA
GO:0042800	Function	Histone H3K4 methyltransferase activity	IDA	20862685
GO:0042800	Function	Histone H3K4 methyltransferase activity	IEA
GO:0048188	Component	Set1C/COMPASS complex	IBA
GO:0048188	Component	Set1C/COMPASS complex	IDA	17998332, 18838538
GO:0048188	Component	Set1C/COMPASS complex	IEA
GO:0048188	Component	Set1C/COMPASS complex	IPI	23508102
GO:0048188	Component	Set1C/COMPASS complex	TAS	27141965
GO:0061629	Function	RNA polymerase II-specific DNA-binding transcription factor binding	IPI	27141965
GO:0140938	Function	Histone H3 methyltransferase activity	IEA
GO:0140945	Function	Histone H3K4 monomethyltransferase activity	IEA
GO:0140999	Function	Histone H3K4 trimethyltransferase activity	IEA
GO:1902036	Process	Regulation of hematopoietic stem cell differentiation	IDA	27141965
GO:1902275	Process	Regulation of chromatin organization	IDA	27141965

Other IDs

• MIM: 611052
• HGNC: 29010
• e!Ensembl: ENSG00000099381

Protein

• UniProt ID: O15047
• Protein name: Histone-lysine N-methyltransferase SETD1A (EC 2.1.1.364) (Lysine N-methyltransferase 2F) (SET domain-containing protein 1A) (hSET1A) (Set1/Ash2 histone methyltransferase complex subunit SET1)
• Protein function: Histone methyltransferase that catalyzes methyl group transfer from S-adenosyl-L-methionine to the epsilon-amino group of 'Lys-4' of histone H3 (H3K4) via a non-processive mechanism (PubMed:12670868, PubMed:25561738). Part of chromatin remodelin
• PDB: 3S8S, 3UVN, 4EWR, 8ILY
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00076	RRM_1	99 → 166	RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)	Domain
  PF11764	N-SET	1425 → 1562	COMPASS (Complex proteins associated with Set1p) component N	Domain
  PF00856	SET	1579 → 1685	SET domain	Family

• Sequence:

  MDQEGGGDGQKAPSFQWRNYKLIVDPALDPALRRPSQKVYRYDGVHFSVNDSKYIPVEDL
  QDPRCHVRSKNRDFSLPVPKFKLDEFYIGQIPLKEVTFARLNDNVRETFLKDMCRKYGEV
  EEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIKGQQRMKYY
  ELIVNGSYTPQTVPTGGKALSEKFQGSGAATETAESRRRSSSDTAAYPAGTTAVGTPGNG
  TPCSQDTSFSSSRQDTPSSFGQFTPQSSQGTPYTSRGSTPYSQDSAYSSSTTSTSFKPRR
  SENSYQDAFSRRHFSASSASTTASTAIAATTAATASSSASSSSLSSSSSSSSSSSSSQFR
  SSDANYPAYYESWNRYQRHTSYPPRRATREEPPGAPFAENTAERFPPSYTSYLPPEPSRP
  TDQDYRPPASEAPPPEPPEPGGGGGGGGPSPEREEVRTSPRPASPARSGSPAPETTNESV
  PFAQHSSLDSRIEMLLKEQRSKFSFLASDTEEEEENSSMVLGARDTGSEVPSGSGHGPCT
  PPPAPANFEDVAPTGSGEPGATRESPKANGQNQASPCSSGDDMEISDDDRGGSPPPAPTP
  PQQPPPPPPPPPPPPPYLASLPLGYPPHQPAYLLPPRPDGPPPPEYPPPPPPPPHIYDFV
  NSLELMDRLGAQWGGMPMSFQMQTQMLTRLHQLRQGKGLIAASAGPPGGAFGEAFLPFPP
  PQEAAYGLPYALYAQGQEGRGAYSREAYHLPMPMAAEPLPSSSVSGEEARLPPREEAELA
  EGKTLPTAGTVGRVLAMLVQEMKSIMQRDLNRKMVENVAFGAFDQWWESKEEKAKPFQNA
  AKQQAKEEDKEKTKLKEPGLLSLVDWAKSGGTTGIEAFAFGSGLRGALRLPSFKVKRKEP
  SEISEASEEKRPRPSTPAEEDEDDPEQEKEAGEPGRPGTKPPKRDEERGKTQGKHRKSFA
  LDSEGEEASQESSSEKDEEDDEEDEEDEDREEAVDTTKKETEVSDGEDEESDSSSKCSLY
  ADSDGENDSTSDSESSSSSSSSSSSSSSSSSSSSSSSSESSSEDEEEEERPAALPSASPP
  PREVPVPTPAPVEVPVPERVAGSPVTPLPEQEASPARPAGPTEESPPSAPLRPPEPPAGP
  PAPAPRPDERPSSPIPLLPPPKKRRKTVSFSAIEVVPAPEPPPATPPQAKFPGPASRKAP
  RGVERTIRNLPLDHASLVKSWPEEVSRGGRSRAGGRGRLTEEEEAEPGTEVDLAVLADLA
  LTPARRGLPALPAVEDSEATETSDEAERPRPLLSHILLEHNYALAVKPTPPAPALRPPEP
  VPAPAALFSSPADEVLEAPEVVVAEAEEPKPQQLQQQREEGEEEGEEEGEEEEEESSDSS
  SSSDGEGALRRRSLRSHARRRRPPPPPPPPPPRAYEPRSEFEQMTILYDIWNSGLDSEDM
  SYLRLTYERLLQQTSGADWLNDTHWVHHTITNLTTPKRKRRPQDGPREHQTGSARSEGYY
  PISKKEKDKYLDVCPVSARQLEGVDTQGTNRVLSERRSEQRRLLSAIGTSAIMDSDLLKL
  NQLKFRKKKLRFGRSRIHEWGLFAMEPIAADEMVIEYVGQNIRQMVADMREKRYVQEGIG
  SSYLFRVDHDTIIDATKCGNLARFINHCCTPNCYAKVITIESQKKIVIYSKQPIGVDEEI
  TYDYKFPLEDNKIPCLCGTESCRGSLN

• Sequence length: 1707

Pathways

KEGG:

Lysine degradation
Metabolic pathways

Reactome:

PKMTs methylate histone lysines
RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function

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
Autism spectrum disorder	Likely pathogenic	rs2543876108	RCV003127372	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Epilepsy, early-onset, with or without developmental delay	Likely pathogenic; Pathogenic	rs2143509708, rs61744449, rs2543861155, rs2056158149, rs755127868, rs2056165149, rs2056100951, rs781482552, rs2056003750, rs2056118338	RCV002225059 RCV002289157 RCV004783056 RCV004783064 RCV001788230 RCV001034711 RCV001034712 RCV001034713 RCV001250554 RCV001254164	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Intellectual disability	Likely pathogenic	rs2056144779	RCV001257739	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neurodevelopmental disorder	Pathogenic	rs2143491920	RCV002273265	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neurodevelopmental disorder with dysmorphic facies and distal limb anomalies	Pathogenic	rs2543874648	RCV003128089	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neurodevelopmental disorder with speech impairment and dysmorphic facies	Likely pathogenic; Pathogenic	rs2056114867, rs2143514019, rs2143509708, rs2543831672, rs2543866311, rs2543909603, rs2543847896, rs2543859166, rs2543833500, rs2543908638, rs2543861155, rs2056158149, rs2543876266, rs2543862825, rs755127868, rs2056360507, rs2056124989, rs2056111688	RCV001706797 RCV001814628 RCV002225059 RCV002287616 RCV002294587 RCV002468784 RCV002510552 RCV003140421 RCV003155649 RCV003314301 RCV004783056 RCV003444528 RCV003493275 RCV003985227 RCV001775121 RCV001261422 RCV001261423 RCV001261424	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Schizophrenia	Pathogenic	rs2056099559, rs869312829, rs869312830, rs770913157, rs869312832, rs869312831	RCV001801339 RCV000210278 RCV000210255 RCV000210257 RCV000210279 RCV000210263	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
SETD1A-related disorder	Likely pathogenic	rs1567353500	RCV003420945	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ANKYLOSING SPONDYLITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDERS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHRONIC OBSTRUCTIVE PULMONARY DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CROHN'S DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEVELOPMENTAL DISABILITIES	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Developmental disorder	Likely benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EPILEPSY, EARLY-ONSET, 2, WITH OR WITHOUT DEVELOPMENTAL DELAY	—	Disgenet, HPO Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GRAVES DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MULTIPLE SCLEROSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURODEVELOPMENTAL DISORDERS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-SPECIFIC SYNDROMIC INTELLECTUAL DISABILITY	—	Disgenet, Orphanet Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PARKINSON DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PSORIASIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PSORIASIS VULGARIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCLEROSING CHOLANGITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ULCERATIVE COLITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adenocarcinoma	Adenocarcinoma	BEFREE	30377207		★☆☆☆☆ Found in Text Mining only
Ankylosing spondylitis	Ankylosing Spondylitis	GWASCAT_DG	26974007		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Apraxias	Apraxia	Pubtator	29463886, 36117209, 40225914	Associate	★☆☆☆☆ Found in Text Mining only
Arthritis Psoriatic	Psoriatic arthritis	Pubtator	20862685	Associate	★☆☆☆☆ Found in Text Mining only
Arthritis Rheumatoid	Rheumatoid arthritis	Pubtator	35479077	Associate	★☆☆☆☆ Found in Text Mining only
Autism Spectrum Disorders	Autism Spectrum Disorder	BEFREE	26938441, 31808517		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autistic Disorder	Autism	Pubtator	26938441	Associate	★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	30191958, 31253781		★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	30191958, 30990809, 31253781, 33223203, 35966598	Associate	★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	31897900	Stimulate	★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	36707804	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	27656834, 32918976, 37581938	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma of lung	Lung carcinoma	BEFREE	24598366		★☆☆☆☆ Found in Text Mining only
Carcinoma Pancreatic Ductal	Pancreatic ductal carcinoma	Pubtator	36271761	Stimulate	★☆☆☆☆ Found in Text Mining only
Carcinoma, Ovarian Epithelial	Ovarian Epithelial carcinoma	BEFREE	26747452		★☆☆☆☆ Found in Text Mining only
Cholangiocarcinoma	Cholangiocarcinoma	BEFREE	31846841		★☆☆☆☆ Found in Text Mining only
Cholangitis, Sclerosing	Cholangitis	GWASCAT_DG	26974007		★☆☆☆☆ Found in Text Mining only
Cognition Disorders	Cognitive disorder	BEFREE	31606247		★☆☆☆☆ Found in Text Mining only
Coloboma	Coloboma	Pubtator	36672956	Associate	★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	24948597	Stimulate	★☆☆☆☆ Found in Text Mining only
Congenital contractural arachnodactyly	Congenital Contractural Arachnodactyly	BEFREE	31846841		★☆☆☆☆ Found in Text Mining only
Crohn Disease	Crohn Disease	GWASCAT_DG	26974007		★☆☆☆☆ Found in Text Mining only
Deep Vein Thrombosis	Thrombosis	BEFREE	22214734		★☆☆☆☆ Found in Text Mining only
Dementia	Dementia	Pubtator	37328865	Associate	★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Development Disorder	BEFREE	26974950, 31197650		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Developmental Disabilities	Development Disorder	GENOMICS_ENGLAND_DG	26974950		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Developmental Disabilities	Developmental disability	Pubtator	27563068	Inhibit	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Developmental Disabilities	Developmental disability	Pubtator	40225914	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Dysmorphic features	Dysmorphic Features	CLINVAR_DG	16921172, 19700006, 24550110, 24853937, 26974950, 28135719		★☆☆☆☆ Found in Text Mining only
Epilepsy	Epilepsy	GENOMICS_ENGLAND_DG	31197650		★☆☆☆☆ Found in Text Mining only
Epithelial ovarian cancer	Ovarian cancer	BEFREE	26747452		★☆☆☆☆ Found in Text Mining only
Eye Diseases	Eye disease	Pubtator	36672956	Associate	★☆☆☆☆ Found in Text Mining only
Facial Dysmorphism with Multiple Malformations	Facial dysmorphism syndrome	Pubtator	40225914	Associate	★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	Pubtator	37974198	Associate	★☆☆☆☆ Found in Text Mining only
Graves Disease	Graves Disease	BEFREE	31341471		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Heart Defects Congenital	Congenital heart defect	Pubtator	37000069	Associate	★☆☆☆☆ Found in Text Mining only
Hematologic Neoplasms	Hematologic Neoplasms	BEFREE	28375985, 31251903		★☆☆☆☆ Found in Text Mining only
Impaired cognition	Impaired Cognition	BEFREE	31606247		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	GENOMICS_ENGLAND_DG	26974950		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual Disability	Intellectual developmental disorder	Pubtator	40225914	Associate	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Language Development Disorders	Language development disorders	Pubtator	40225914	Associate	★☆☆☆☆ Found in Text Mining only
leukemia	Leukemia	BEFREE	15199122, 20236310		★☆☆☆☆ Found in Text Mining only
Leukemia	Leukemia	Pubtator	36450243, 37535603	Associate	★☆☆☆☆ Found in Text Mining only
Leukemia Myeloid Acute	Myeloid leukemia	Pubtator	27563068	Inhibit	★☆☆☆☆ Found in Text Mining only
Leukemia Myeloid Acute	Myeloid leukemia	Pubtator	36450243	Associate	★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	BEFREE	29474905		★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung neoplasms	Pubtator	34219384	Associate	★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus Systemic	Systemic lupus erythematosus	Pubtator	27904655	Associate	★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus, Systemic	Lupus Erythematosus	BEFREE	27904655		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	30191958, 31253781		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	24598366		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of pancreas	Pancreatic cancer	BEFREE	31237042		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	16152623, 28385531, 30221689		★☆☆☆☆ Found in Text Mining only
Mammary Neoplasms	Mammary Neoplasms	BEFREE	30191958		★☆☆☆☆ Found in Text Mining only
Microphthalmos	Microphthalmos	Pubtator	36672956	Associate	★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	31253781, 31564898		★☆☆☆☆ Found in Text Mining only
Neurodevelopmental Disorders	Neurodevelopmental Disorders	BEFREE	26974950, 31197650		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Obsessive-Compulsive Disorder	Obsessive-Compulsive Disorder	BEFREE	31808517		★☆☆☆☆ Found in Text Mining only
Oestrogen receptor positive breast cancer	Oestrogen Receptor Positive Breast Cancer	BEFREE	30191958		★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Ovarian neoplasm	Pubtator	36707804	Associate	★☆☆☆☆ Found in Text Mining only
Pancreatic carcinoma	Pancreatic carcinoma	BEFREE	31237042		★☆☆☆☆ Found in Text Mining only
Parkinson Disease	Parkinson disease	BEFREE	28586827		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Parkinson Disease	Parkinson disease	Pubtator	28586827, 37328865	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Prostatic Neoplasms	Prostatic neoplasm	Pubtator	27268279, 33050986	Associate	★☆☆☆☆ Found in Text Mining only
Psoriasis	Psoriasis	GWASCAT_DG	26974007		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Schizophrenia	BEFREE	24853937, 26938441, 26974950, 27482034, 31606247		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Schizophrenia	Schizophrenia	PSYGENET_DG	24853937		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Schizophrenia	Schizophrenia	Pubtator	26938441, 29228394	Associate	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Schizophrenia	Schizophrenia	CLINVAR_DG	26974950		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Schizophrenia	Schizophrenia	GENOMICS_ENGLAND_DG	26974950		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Severe myopia	Myopia	BEFREE	22857148		★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma	Carcinoma	BEFREE	30377207		★☆☆☆☆ Found in Text Mining only
Triple Negative Breast Neoplasms	Triple negative breast cancer	Pubtator	30191958	Associate	★☆☆☆☆ Found in Text Mining only
Triple Negative Breast Neoplasms	Triple Negative Breast Neoplasms	BEFREE	31552595		★☆☆☆☆ Found in Text Mining only
Ulcerative Colitis	Ulcerative colitis	GWASCAT_DG	26974007		★★☆☆☆ Found in Text Mining + Unknown/Other Associations