BEGAIN

brain enriched guanylate kinase associated

Basic information

Region (hg38): 14:100537147-100587417

Links

ENSG00000183092 ∙ NCBI:57596 ∙ OMIM:618597 ∙ HGNC:24163 ∙ Uniprot:Q9BUH8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BEGAIN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BEGAIN gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			23		2	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	3

Variants in BEGAIN

This is a list of pathogenic ClinVar variants found in the BEGAIN region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
14-100538043-G-C		not specified	Uncertain significance (Apr 12, 2023)
14-100538096-G-C		not specified	Uncertain significance (Feb 07, 2023)
14-100538175-C-G		not specified	Uncertain significance (Sep 26, 2024)
14-100538178-C-T		not specified	Uncertain significance (Jan 31, 2024)
14-100538198-C-G		not specified	Uncertain significance (Oct 26, 2021)
14-100538198-C-T		not specified	Uncertain significance (Aug 01, 2024)
14-100538200-C-G		not specified	Uncertain significance (May 12, 2024)
14-100538218-G-A			Benign (Jun 14, 2018)
14-100538237-C-T		not specified	Uncertain significance (Sep 15, 2021)
14-100538259-C-T		not specified	Uncertain significance (Feb 28, 2024)
14-100538394-C-G		not specified	Uncertain significance (Nov 09, 2024)
14-100538397-C-G		not specified	Uncertain significance (Apr 13, 2022)
14-100538399-C-A		not specified	Uncertain significance (Aug 27, 2024)
14-100538402-C-A		not specified	Uncertain significance (Jan 02, 2024)
14-100538439-G-A		not specified	Uncertain significance (Dec 05, 2022)
14-100538567-G-T		not specified	Uncertain significance (Jun 22, 2023)
14-100538571-G-A		not specified	Uncertain significance (Jun 06, 2022)
14-100538634-A-T		not specified	Uncertain significance (Aug 17, 2021)
14-100538643-G-A		not specified	Uncertain significance (Jun 03, 2022)
14-100538646-C-T		Marfanoid habitus and intellectual disability • not specified	Uncertain significance (Apr 19, 2024)
14-100538649-A-G		not specified	Uncertain significance (May 07, 2024)
14-100538664-C-T		not specified	Uncertain significance (Mar 01, 2024)
14-100538939-T-A		not specified	Uncertain significance (Jun 18, 2024)
14-100538954-G-C		not specified	Uncertain significance (Jul 14, 2021)
14-100538978-C-G		not specified	Uncertain significance (Jul 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BEGAIN	protein_coding	protein_coding	ENST00000443071	6	50265

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.970	0.0300	125039	0	4	125043	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.24	254	376	0.675	0.0000263	3745
Missense in Polyphen		64	126.68	0.50522		1377
Synonymous	0.904	162	177	0.914	0.0000142	1184
Loss of Function	3.69	2	19.7	0.102	0.00000102	231

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000293	0.0000293
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000283	0.0000266
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May sustain the structure of the postsynaptic density (PSD).
• Pathway: Neuronal System;Neurexins and neuroligins;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.0838
• rvis_EVS: -0.6
• rvis_percentile_EVS: 18.06

Haploinsufficiency Scores

• pHI: 0.154
• hipred: Y
• hipred_score: 0.806
• ghis: 0.572

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.544

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Begain

Gene ontology

• Cellular component: cytoplasm;membrane
• Molecular function: protein binding