SRGAP3

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

Basic information

Region (hg38): 3:8980590-9363053

Previous symbols: [ "SRGAP2" ]

Links

ENSG00000196220 ∙ NCBI:9901 ∙ OMIM:606525 ∙ HGNC:19744 ∙ Uniprot:O43295 ∙ 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 SRGAP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SRGAP3 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				20	10	30
missense			59	2	3	64
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding				2	1	3
Total	0	0	59	24	14

Variants in SRGAP3

This is a list of pathogenic ClinVar variants found in the SRGAP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-8985530-C-T		not specified	Uncertain significance (Mar 31, 2024)
3-8985547-C-A		not specified	Uncertain significance (Jan 04, 2022)
3-8985562-T-A		not specified	Uncertain significance (Mar 29, 2024)
3-8985578-C-T		SRGAP3-related disorder	Benign (Dec 31, 2019)
3-8985597-C-T			Likely benign (Feb 25, 2018)
3-8985623-G-A		not specified	Uncertain significance (Jun 24, 2022)
3-8985641-C-A		not specified	Uncertain significance (Dec 07, 2023)
3-8985653-G-T		not specified	Uncertain significance (Nov 12, 2021)
3-8985656-G-A		not specified	Uncertain significance (Mar 01, 2023)
3-8985687-G-A			Likely benign (Apr 12, 2018)
3-8985742-C-T		See cases	Uncertain significance (Dec 04, 2019)
3-8985749-C-A		not specified	Uncertain significance (Jan 23, 2023)
3-8985749-C-T		SRGAP3-related disorder	Uncertain significance (Oct 02, 2023)
3-8985783-G-A		SRGAP3-related disorder	Benign (Dec 31, 2019)
3-8990527-G-A			Likely benign (Jun 01, 2022)
3-8990581-C-T		SRGAP3-related disorder	Benign/Likely benign (Oct 28, 2019)
3-8990637-C-T		not specified	Uncertain significance (Jun 29, 2022)
3-8990663-C-T		not specified	Uncertain significance (Nov 05, 2021)
3-8990666-T-C		not specified	Uncertain significance (May 03, 2023)
3-8990703-T-A		not specified	Uncertain significance (Feb 07, 2023)
3-8990718-T-C		SRGAP3-related disorder	Benign (Dec 31, 2019)
3-8990735-C-T		not specified	Uncertain significance (Jan 16, 2024)
3-8990736-G-A		not specified	Uncertain significance (Nov 15, 2021)
3-8990744-G-A		not specified	Uncertain significance (Aug 04, 2023)
3-8990764-G-T		SRGAP3-related disorder	Likely benign (Mar 11, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SRGAP3	protein_coding	protein_coding	ENST00000383836	22	382463

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000298	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.11	516	670	0.770	0.0000439	7256
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000206	0.000206
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000445	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

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}.
• Pathway: Axon guidance - Homo sapiens (human);Developmental Biology;Signal Transduction;Rho GTPase cycle;Inactivation of CDC42 and RAC1;Signaling by Rho GTPases;Signaling by ROBO receptors;Axon guidance (Consensus)

Recessive Scores

• pRec: 0.142

Intolerance Scores

• loftool: 0.303
• rvis_EVS: -1.64
• rvis_percentile_EVS: 2.84

Haploinsufficiency Scores

• pHI: 0.291
• hipred: Y
• hipred_score: 0.749
• ghis: 0.621

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.424

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Srgap3
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype

Gene ontology

• Biological process: signal transduction;negative regulation of cell migration;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction
• Cellular component: cytoplasm;cytosol
• Molecular function: GTPase activator activity;protein binding;Rac GTPase binding