NBEA (neurobeachin)

Gene

• Entrez ID: 26960
• Gene name: Neurobeachin
• Gene symbol: NBEA
• Synonyms (NCBI Gene): BCL8B, LYST2, NEDEGE
• Chromosome: 13
• Chromosome location: 13q13.3
• Summary: This gene encodes a member of a large, diverse group of A-kinase anchor proteins that target the activity of protein kinase A to specific subcellular sites by binding to its type II regulatory subunits. Brain-specific expression and coat protein-like memb

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs869312667	C>T	Likely-pathogenic	Coding sequence variant, genic upstream transcript variant, missense variant
rs878853169	C>T	Likely-pathogenic	Coding sequence variant, stop gained
rs1594162606	G>A	Likely-pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT016246	hsa-miR-548b-3p	Sequencing	20371350
MIRT016751	hsa-miR-335-5p	Microarray	18185580
MIRT021372	hsa-miR-9-5p	Microarray	17612493
MIRT021882	hsa-miR-128-3p	Microarray	17612493
MIRT030706	hsa-miR-21-5p	Microarray	18591254
MIRT050693	hsa-miR-18a-5p	CLASH	23622248
MIRT036648	hsa-miR-935	CLASH	23622248
MIRT440143	hsa-miR-409-5p	HITS-CLIP	24374217
MIRT440141	hsa-miR-127-3p	HITS-CLIP	24374217
MIRT440140	hsa-miR-485-3p	HITS-CLIP	24374217
MIRT440139	hsa-miR-377-3p	HITS-CLIP	24374217
MIRT440143	hsa-miR-409-5p	HITS-CLIP	24374217
MIRT440141	hsa-miR-127-3p	HITS-CLIP	24374217
MIRT440140	hsa-miR-485-3p	HITS-CLIP	24374217
MIRT440139	hsa-miR-377-3p	HITS-CLIP	24374217
MIRT1174728	hsa-miR-1	CLIP-seq
MIRT1174729	hsa-miR-137	CLIP-seq
MIRT1174730	hsa-miR-1909	CLIP-seq
MIRT1174731	hsa-miR-206	CLIP-seq
MIRT1174732	hsa-miR-3134	CLIP-seq
MIRT1174733	hsa-miR-3668	CLIP-seq
MIRT1174734	hsa-miR-3671	CLIP-seq
MIRT1174735	hsa-miR-3673	CLIP-seq
MIRT1174736	hsa-miR-3943	CLIP-seq
MIRT1174737	hsa-miR-4313	CLIP-seq
MIRT1174738	hsa-miR-4455	CLIP-seq
MIRT1174739	hsa-miR-4534	CLIP-seq
MIRT1174740	hsa-miR-4711-3p	CLIP-seq
MIRT1174741	hsa-miR-4731-5p	CLIP-seq
MIRT1174742	hsa-miR-491-3p	CLIP-seq
MIRT1174743	hsa-miR-544	CLIP-seq
MIRT1174744	hsa-miR-607	CLIP-seq
MIRT1174745	hsa-miR-609	CLIP-seq
MIRT1174746	hsa-miR-613	CLIP-seq
MIRT1174747	hsa-miR-129-5p	CLIP-seq
MIRT1174748	hsa-miR-342-3p	CLIP-seq
MIRT1174749	hsa-miR-377	CLIP-seq
MIRT2050548	hsa-miR-1273e	CLIP-seq
MIRT2050549	hsa-miR-4666-5p	CLIP-seq
MIRT2050550	hsa-miR-624	CLIP-seq
MIRT2279712	hsa-miR-197	CLIP-seq
MIRT2279713	hsa-miR-4695-3p	CLIP-seq
MIRT2279714	hsa-miR-5096	CLIP-seq
MIRT2279715	hsa-miR-513c	CLIP-seq
MIRT2279716	hsa-miR-514b-5p	CLIP-seq
MIRT2431500	hsa-miR-338-5p	CLIP-seq
MIRT2279715	hsa-miR-513c	CLIP-seq
MIRT2279716	hsa-miR-514b-5p	CLIP-seq
MIRT2431501	hsa-miR-642b	CLIP-seq
MIRT2431500	hsa-miR-338-5p	CLIP-seq
MIRT2438861	hsa-miR-4757-3p	CLIP-seq
MIRT2465692	hsa-miR-4433	CLIP-seq
MIRT2050548	hsa-miR-1273e	CLIP-seq
MIRT2279712	hsa-miR-197	CLIP-seq
MIRT2578304	hsa-miR-21	CLIP-seq
MIRT2578305	hsa-miR-300	CLIP-seq
MIRT2578306	hsa-miR-3126-3p	CLIP-seq
MIRT2578307	hsa-miR-3128	CLIP-seq
MIRT2578308	hsa-miR-3185	CLIP-seq
MIRT2578309	hsa-miR-331-3p	CLIP-seq
MIRT2431500	hsa-miR-338-5p	CLIP-seq
MIRT1174749	hsa-miR-377	CLIP-seq
MIRT2578310	hsa-miR-381	CLIP-seq
MIRT2578311	hsa-miR-383	CLIP-seq
MIRT2578312	hsa-miR-4292	CLIP-seq
MIRT1174738	hsa-miR-4455	CLIP-seq
MIRT2578313	hsa-miR-4477b	CLIP-seq
MIRT2578314	hsa-miR-450b-5p	CLIP-seq
MIRT2578315	hsa-miR-4666-3p	CLIP-seq
MIRT2050549	hsa-miR-4666-5p	CLIP-seq
MIRT2279713	hsa-miR-4695-3p	CLIP-seq
MIRT2578316	hsa-miR-4704-3p	CLIP-seq
MIRT2578317	hsa-miR-4720-3p	CLIP-seq
MIRT2578318	hsa-miR-4720-5p	CLIP-seq
MIRT2438861	hsa-miR-4757-3p	CLIP-seq
MIRT2578319	hsa-miR-4760-3p	CLIP-seq
MIRT2578320	hsa-miR-4772-5p	CLIP-seq
MIRT2578321	hsa-miR-4799-3p	CLIP-seq
MIRT2578322	hsa-miR-494	CLIP-seq
MIRT2279714	hsa-miR-5096	CLIP-seq
MIRT2279715	hsa-miR-513c	CLIP-seq
MIRT2279716	hsa-miR-514b-5p	CLIP-seq
MIRT2578323	hsa-miR-520d-5p	CLIP-seq
MIRT2578324	hsa-miR-524-5p	CLIP-seq
MIRT2578325	hsa-miR-568	CLIP-seq
MIRT2578326	hsa-miR-590-5p	CLIP-seq
MIRT1174745	hsa-miR-609	CLIP-seq
MIRT2431501	hsa-miR-642b	CLIP-seq
MIRT2578305	hsa-miR-300	CLIP-seq
MIRT2685854	hsa-miR-3148	CLIP-seq
MIRT2578308	hsa-miR-3185	CLIP-seq
MIRT2578309	hsa-miR-331-3p	CLIP-seq
MIRT2431500	hsa-miR-338-5p	CLIP-seq
MIRT2685855	hsa-miR-3688-3p	CLIP-seq
MIRT2578310	hsa-miR-381	CLIP-seq
MIRT2578311	hsa-miR-383	CLIP-seq
MIRT2578312	hsa-miR-4292	CLIP-seq
MIRT1174738	hsa-miR-4455	CLIP-seq
MIRT2578315	hsa-miR-4666-3p	CLIP-seq
MIRT2050549	hsa-miR-4666-5p	CLIP-seq
MIRT2578316	hsa-miR-4704-3p	CLIP-seq
MIRT2438861	hsa-miR-4757-3p	CLIP-seq
MIRT2578319	hsa-miR-4760-3p	CLIP-seq
MIRT2578320	hsa-miR-4772-5p	CLIP-seq
MIRT2578322	hsa-miR-494	CLIP-seq
MIRT2279715	hsa-miR-513c	CLIP-seq
MIRT2279716	hsa-miR-514b-5p	CLIP-seq
MIRT2578323	hsa-miR-520d-5p	CLIP-seq
MIRT2578324	hsa-miR-524-5p	CLIP-seq
MIRT2578325	hsa-miR-568	CLIP-seq
MIRT2685856	hsa-miR-579	CLIP-seq
MIRT1174745	hsa-miR-609	CLIP-seq
MIRT2431501	hsa-miR-642b	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005737	Component	Cytoplasm	IEA
GO:0005802	Component	Trans-Golgi network	ISS
GO:0005829	Component	Cytosol	IBA
GO:0005829	Component	Cytosol	ISS
GO:0005886	Component	Plasma membrane	ISS
GO:0008104	Process	Intracellular protein localization	IBA
GO:0012505	Component	Endomembrane system	ISS
GO:0016020	Component	Membrane	IBA
GO:0016020	Component	Membrane	IEA
GO:0019901	Function	Protein kinase binding	IBA

Other IDs

• MIM: 604889
• HGNC: 7648
• e!Ensembl: ENSG00000172915

Protein

• UniProt ID: Q8NFP9
• Protein name: Neurobeachin (Lysosomal-trafficking regulator 2) (Protein BCL8B)
• Protein function: Binds to type II regulatory subunits of protein kinase A and anchors/targets them to the membrane. May anchor the kinase to cytoskeletal and/or organelle-associated proteins (By similarity).
• PDB: 1MI1
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF13385	Laminin_G_3	238 → 403		Domain
  PF15787	DUF4704	472 → 743	Domain of unknown function (DUF4704)	Family
  PF06469	DUF1088	1966 → 2132	Domain of Unknown Function (DUF1088)	Family
  PF14844	PH_BEACH	2158 → 2255	PH domain associated with Beige/BEACH	Domain
  PF02138	Beach	2287 → 2563	Beige/BEACH domain	Family

• Tissue specificity: TISSUE SPECIFICITY: Predominant in many brain structures. Also expressed at medium levels in spleen, thymus, prostate, testis and ovary. Low level expression is seen in heart, kidney, pancreas, skeletal muscle and intestine. {ECO:0000269|PubMed:12160729}.
• Sequence:

  MASEKPGPGPGLEPQPVGLIAVGAAGGGGGGSGGGGTGGSGMGELRGASGSGSVMLPAGM
  INPSVPIRNIRMKFAVLIGLIQVGEVSNRDIVETVLNLLVGGEFDLEMNFIIQDAESITC
  MTELLEHCDVTCQAEIWSMFTAILRKSVRNLQTSTEVGLIEQVLLKMSAVDDMIADLLVD
  MLGVLASYSITVKELKLLFSMLRGESGIWPRHAVKLLSVLNQMPQRHGPDTFFNFPGCSA
  AAIALPPIAKWPYQNGFTLNTWFRMDPLNNINVDKDKPYLYCFRTSKGVGYSAHFVGNCL
  IVTSLKSKGKGFQHCVKYDFQPRKWYMISIVHIYNRWRNSEIRCYVNGQLVSYGDMAWHV
  NTNDSYDKCFLGSSETADANRVFCGQLGAVYVFSEALNPAQIFAIHQLGPGYKSTFKFKS
  ESDIHLAEHHKQVLYDGKLASSIAFTYNAKATDAQLCLESSPKENASIFVHSPHALMLQD
  VKAIVTHSIHSAIHSIGGIQVLFPLFAQLDNRQLNDSQVETTVCATLLAFLVELLKSSVA
  MQEQMLGGKGFLVIGYLLEKSSRVHITRAVLEQFLSFAKYLDGLSHGAPLLKQLCDHILF
  NPAIWIHTPAKVQLSLYTYLSAEFIGTATIYTTIRRVGTVLQLMHTLKYYYWVINPADSS
  GITPKGLDGPRPSQKEIISLRAFMLLFLKQLILKDRGVKEDELQSILNYLLTMHEDENIH
  DVLQLLVALMSEHPASMIPAFDQRNGIRVIYKLLASKSESIWVQALKVLGYFLKHLGHKR
  KVEIMHTHSLFTLLGERLMLHTNTVTVTTYNTLYEILTEQVCTQVVHKPHPEPDSTVKIQ
  NPMILKVVATLLKNSTPSAELMEVRRLFLSDMIKLFSNSRENRRCLLQCSVWQDWMFSLG
  YINPKNSEEQKITEMVYNIFRILLYHAIKYEWGGWRVWVDTLSIAHSKVTYEAHKEYLAK
  MYEEYQRQEEENIKKGKKGNVSTISGLSSQTTGAKGGMEIREIEDLSQSQSPESETDYPV
  STDTRDLLMSTKVSDDILGNSDRPGSGVHVEVHDLLVDIKAEKVEATEVKLDDMDLSPET
  LVGGENGALVEVESLLDNVYSAAVEKLQNNVHGSVGIIKKNEEKDNGPLITLADEKEDLP
  NSSTSFLFDKIPKQEEKLLPELSSNHIIPNIQDTQVHLGVSDDLGLLAHMTGSVDLTCTS
  SIIEEKEFKIHTTSDGMSSISERDLASSTKGLEYAEMTATTLETESSSSKIVPNIDAGSI
  ISDTERSDDGKESGKEIRKIQTTTTTQAVQGRSITQQDRDLRVDLGFRGMPMTEEQRRQF
  SPGPRTTMFRIPEFKWSPMHQRLLTDLLFALETDVHVWRSHSTKSVMDFVNSNENIIFVH
  NTIHLISQMVDNIIIACGGILPLLSAATSPTGSKTELENIEVTQGMSAETAVTFLSRLMA
  MVDVLVFASSLNFSEIEAEKNMSSGGLMRQCLRLVCCVAVRNCLECRQRQRDRGNKSSHG
  SSKPQEVPQSVTATAASKTPLENVPGNLSPIKDPDRLLQDVDINRLRAVVFRDVDDSKQA
  QFLALAVVYFISVLMVSKYRDILEPQRETTRTGSQPGRNIRQEINSPTSTVVVIPSIPHP
  SLNHGFLAKLIPEQSFGHSFYKETPAAFPDTIKEKETPTPGEDIQVESSIPHTDSGIGEE
  QVASILNGAELETSTGPDAMSELLSTLSSEVKKSQESLTENPSETLKPATSISSISQTKG
  INVKEILKSLVAAPVEIAECGPEPIPYPDPALKRETQAILPMQFHSFDRSVVVPVKKPPP
  GSLAVTTVGATTAGSGLPTGSTSNIFAATGATPKSMINTTGAVDSGSSSSSSSSSFVNGA
  TSKNLPAVQTVAPMPEDSAENMSITAKLERALEKVAPLLREIFVDFAPFLSRTLLGSHGQ
  ELLIEGLVCMKSSTSVVELVMLLCSQEWQNSIQKNAGLAFIELINEGRLLCHAMKDHIVR
  VANEAEFILNRQRAEDVHKHAEFESQCAQYAADRREEEKMCDHLISAAKHRDHVTANQLK
  QKILNILTNKHGAWGAVSHSQLHDFWRLDYWEDDLRRRRRFVRNAFGSTHAEALLKAAIE
  YGTEEDVVKSKKTFRSQAIVNQNAETELMLEGDDDAVSLLQEKEIDNLAGPVVLSTPAQL
  IAPVVVAKGTLSITTTEIYFEVDEDDSAFKKIDTKVLAYTEGLHGKWMFSEIRAVFSRRY
  LLQNTALEVFMANRTSVMFNFPDQATVKKVVYSLPRVGVGTSYGLPQARRISLATPRQLY
  KSSNMTQRWQRREISNFEYLMFLNTIAGRTYNDLNQYPVFPWVLTNYESEELDLTLPGNF
  RDLSKPIGALNPKRAVFYAERYETWEDDQSPPYHYNTHYSTATSTLSWLVRIEPFTTFFL
  NANDGKFDHPDRTFSSVARSWRTSQRDTSDVKELIPEFYYLPEMFVNSNGYNLGVREDEV
  VVNDVDLPPWAKKPEDFVRINRMALESEFVSCQLHQWIDLIFGYKQRGPEAVRALNVFHY
  LTYEGSVNLDSITDPVLREAMEAQIQNFGQTPSQLLIEPHPPRSSAMHLCFLPQSPLMFK
  DQMQQDVIMVLKFPSNSPVTHVAANTLPHLTIPAVVTVTCSRLFAVNRWHNTVGLRGAPG
  YSLDQAHHLPIEMDPLIANNSGVNKRQITDLVDQSIQINAHCFVVTADNRYILICGFWDK
  SFRVYSTETGKLTQIVFGHWDVVTCLARSESYIGGDCYIVSGSRDATLLLWYWSGRHHII
  GDNPNSSDYPAPRAVLTGHDHEVVCVSVCAELGLVISGAKEGPCLVHTITGDLLRALEGP
  ENCLFPRLISVSSEGHCIIYYERGRFSNFSINGKLLAQMEINDSTRAILLSSDGQNLVTG
  GDNGVVEVWQACDFKQLYIYPGCDAGIRAMDLSHDQRTLITGMASGSIVAFNIDFNRWHY
  EHQNRY

• Sequence length: 2946

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Autism spectrum disorder	Pathogenic	rs2504151015	RCV003127402
Epilepsy	Pathogenic	rs2070957033	RCV001253529
Intellectual disability	Likely pathogenic; Pathogenic	rs2153082059, rs779780049	RCV001526555 RCV001843756
NBEA-related complex neurodevelopmental disorder	Likely pathogenic	rs2152563427	RCV001797009
NBEA-related developmental delay and generalized epilepsy	Likely pathogenic	rs1594162606	RCV000787957
NBEA-related disorder	Pathogenic; Likely pathogenic	rs1215568155, rs2503620997	RCV003903618 RCV003402807
Neurodevelopmental delay	Pathogenic	rs2070957033	RCV001253529
Neurodevelopmental disorder with or without early-onset generalized epilepsy	Likely pathogenic; Pathogenic	rs763376147, rs2073745817, rs2152930968, rs2503640330, rs2502185013, rs2503639083, rs2549940466, rs2549714620, rs779764549, rs2550006957, rs2503665263, rs2503592299, rs2503578399, rs1265307831, rs1288199769, rs1296627050, rs1594162606, rs2069582666, rs2070635297, rs1275520648, rs2079516243, rs2069590640, rs910146888, rs2085290856	RCV001837426 RCV002250133 RCV002273341 RCV002279892 RCV002472254 RCV003142506 RCV003135330 RCV003130993 RCV003229501 RCV003314321 RCV003314322 RCV003333428 RCV003458934 RCV003761182 RCV003883247 RCV003989453 RCV003992128 RCV002264743 RCV004799396 RCV004594260 RCV001290110 RCV001290111 RCV001290112 RCV001290113 RCV001290114
typical paroxysmal kinesigenic dyskinesia	Pathogenic	rs2085418293	RCV001249901

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Abnormal bleeding	Uncertain significance	rs924269207	RCV001270530
Cervical cancer	Conflicting classifications of pathogenicity; Benign	rs189755961, rs78759625	RCV005905159 RCV005902621
Clear cell carcinoma of kidney	Conflicting classifications of pathogenicity	rs189755961	RCV005905160
Developmental disorder	Likely benign; Uncertain significance	rs2153043712, rs2153065630	RCV001843804 RCV001843825
Familial cancer of breast	Likely benign; Conflicting classifications of pathogenicity	rs183274221, rs189755961	RCV005906353 RCV005905157
Gastric cancer	Likely benign	rs200167940	RCV005929845
Intellectual disability and seizures	Uncertain significance	rs2040043095	RCV001249660
Lung cancer	Likely benign	rs183274221	RCV005906354
Malignant tumor of urinary bladder	Conflicting classifications of pathogenicity	rs189755961	RCV005905158
Melanoma	Conflicting classifications of pathogenicity	rs189755961	RCV005905162
NBEA-related intellectual disability	Uncertain significance	rs2062794117, rs2071378660	RCV001270797 RCV001270798
Neurodevelopmental disorder	Uncertain significance; Conflicting classifications of pathogenicity	rs2152710919, rs2153082051	RCV001374898 RCV001780039
Sarcoma	Benign	rs78759625	RCV005902622
See cases	Uncertain significance; Conflicting classifications of pathogenicity; Likely benign	rs1047295648, rs772494015, rs2152730933, rs962193733, rs2152659253, rs2065444611, rs2152741962, rs372882596, rs370712135, rs2059070502, rs2503193770, rs2549714840, rs2066170655	RCV001420515 RCV001542389 RCV001542370 RCV001542303 RCV001591644 RCV001591674 RCV001591687 RCV001837312 RCV002252840 RCV002252629 RCV004584538 RCV003128500 RCV001196553
Thrombocytopenia	Uncertain significance	rs924269207	RCV001270530
Thyroid cancer, nonmedullary, 1	Conflicting classifications of pathogenicity	rs189755961	RCV005905161
Uterine corpus endometrial carcinoma	Benign	rs78759625	RCV005902623

Associations from Text Mining
Disease Name	Relationship Type	References
Autistic Disorder	Associate	12826745, 30269351
Bipolar Disorder	Associate	25451450
Developmental Disabilities	Associate	34573300
Disease	Associate	30269351
Epilepsies Myoclonic	Associate	30269351
Epilepsy	Associate	30269351
Language Disorders	Associate	12826745
Multiple Myeloma	Associate	19135901