BEGAIN

protein-coding

brain enriched guanylate kinase associated

Gene summary

Predicted to enable kinase activity. Predicted to be involved in evoked excitatory postsynaptic potential. Predicted to be located in dendrite; nucleus; and presynapse. Predicted to be active in glutamatergic synapse and postsynapse. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001385089.1

Inheritance

—

ClinVar variants

U:74B:4

Top phenotype

Marfanoid habitus and intellectual disability

gnomAD constraint

pLI —, LoF o/e 0.1

Max pathogenic AF

—

Genomic locus

chr14:100,537,147-100,587,417

External References & Databases

Ensembl (ENSG00000183092)

Transcript & Mutation Effects

hg38 • Region Span ~50.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to BEGAIN variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 74

not providedTotal: 3

Marfanoid habitus and intellectual disabilityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001385089.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			74 clinvar	1 clinvar	2 clinvar	77
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	74	1	3	78

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 45 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001385089.1	RefSeq	NP_001372018.1	7	MANE Select
ENST00000554140.3	Ensembl	ENSP00000451125.2	7	MANE Select
NM_001159531.2	RefSeq	NP_001153003.1	6	Standard
NM_001385082.1	RefSeq	NP_001372011.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Neuronal System
Neurexins and neuroligins
Protein-protein interactions at synapses

Molecular Function

protein binding

Cellular Component

cytoplasm
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000443071
Coding exons: 6
Length: 50265
Individuals with no LoFs: 125039
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125043
p: 0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.24	254	376	0.675	0.0000263	3745
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000028	0.000027	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May sustain the structure of the postsynaptic density (PSD).;

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.0838
RVIS EVS: -0.6
RVIS percentile EVS: 18.06

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.544

Gene Damage Prediction

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