SRGAP3

protein-coding

SLIT-ROBO Rho GTPase activating protein 3, the group of AH/BAR family Rho GTPase activating proteins|F-BAR domain containing

Gene summary

Predicted to enable GTPase activator activity. Predicted to be involved in negative regulation of cell migration; nervous system development; and regulation of postsynapse assembly. Is active in postsynapse. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

SRGAP2

MANE transcript

NM_014850.4

Inheritance

—

ClinVar variants

P:1U:140B:45

Top phenotype

SRGAP3-related disorder

gnomAD constraint

pLI —, LoF o/e 0.13

Max pathogenic AF

—

Genomic locus

chr3:8,980,591-9,363,053

External References & Databases

Ensembl (ENSG00000196220)

Transcript & Mutation Effects

hg38 • Region Span ~382.5 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 SRGAP3 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 147

not providedTotal: 38

SRGAP3-related disorderTotal: 29

Moyamoya angiopathyTotal: 1

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014850.4. 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			2 clinvar	28 clinvar	8 clinvar	38
missense		1 clinvar	133 clinvar	6 clinvar	3 clinvar	143
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	1	140	34	11	186

Highest pathogenic variant AF is 0.000002736285

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014850.4	RefSeq	NP_055665.1	22	MANE Select
ENST00000383836.8	Ensembl	ENSP00000373347.3	22	MANE Select
NM_001033117.3	RefSeq	NP_001028289.1	22	Standard
ENST00000360413.7	Ensembl	ENSP00000353587.3	22	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Axon guidance - Homo sapiens (human)
Developmental Biology
Signal Transduction
Rho GTPase cycle
Inactivation of CDC42 and RAC1

Biological Process

signal transduction
negative regulation of cell migration
positive regulation of GTPase activity
regulation of small GTPase mediated signal transduction

Molecular Function

GTPase activator activity
protein binding
Rac GTPase binding

Cellular Component

cytoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000383836
Coding exons: 22
Length: 382463
Individuals with no LoFs: 125734
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 125748
p: 0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.11	516	670	0.770	0.0000439	7256
Missense (PolyPhen)		223	334.71	0.66625		3577
Synonymous	-1.26	305	278	1.10	0.0000198	2081
Loss of Function	5.94	7	54.1	0.129	0.00000303	613

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: GTPase-activating protein for RAC1 and perhaps Cdc42, but not for RhoA small GTPase. May attenuate RAC1 signaling in neurons. {ECO:0000269|PubMed:12195014, ECO:0000269|PubMed:12447388}.;
Disease: DISEASE: Note=A chromosomal aberration involving SRGAP3 is found in a patient with severe idiopathic mental retardation (PubMed:12195014). Translocation t(X;3)(p11.2;p25) (PubMed:12195014). {ECO:0000269|PubMed:12195014}.;

Recessive Scores

pRec: 0.142

Intolerance Scores

LoFtool: 0.303
RVIS EVS: -1.64
RVIS percentile EVS: 2.84

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.424

Gene Damage Prediction

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