SH3GLB2

protein-coding

SH3 domain containing GRB2 like, endophilin B2, the group of N-BAR domain containing

Gene summary

Enables identical protein binding activity. Predicted to be involved in membrane organization and postsynaptic neurotransmitter receptor internalization. Located in cytosol. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_020145.4

Inheritance

—

ClinVar variants

U:55B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.41

Max pathogenic AF

—

Genomic locus

chr9:129,007,036-129,028,331

External References & Databases

Ensembl (ENSG00000148341)

Transcript & Mutation Effects

hg38 • Region Span ~21.3 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 SH3GLB2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 48

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020145.4. 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			4 clinvar	1 clinvar	1 clinvar	6
missense			48 clinvar			48
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	55	1	1	57

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 81 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020145.4	RefSeq	NP_064530.1	11	MANE Select
ENST00000372564.8	Ensembl	ENSP00000361645.3	11	MANE Select
NM_001287045.2	RefSeq	NP_001273974.1	13	Standard
NM_001287046.2	RefSeq	NP_001273975.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Endocytosis - Homo sapiens (human)

Molecular Function

protein binding
identical protein binding
cadherin binding

Cellular Component

nucleoplasm
cytoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372564
Coding exons: 11
Length: 21268
Individuals with no LoFs: 125725
Homozygous LoFs: 0
Heterozygous LoFs: 18
Defined: 125743
p: 0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.38	159	216	0.735	0.0000129	2516
Missense (PolyPhen)		66	102.54	0.64366		1221
Synonymous	-1.06	104	91.2	1.14	0.00000579	781
Loss of Function	2.40	8	19.4	0.412	9.23e-7	241

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	0.00017	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00012	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.107

Intolerance Scores

LoFtool: 0.487
RVIS EVS: 0.17
RVIS percentile EVS: 65.96

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.791

Gene Damage Prediction

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