SH3GL3

SH3 domain containing GRB2 like 3, endophilin A3, the group of N-BAR domain containing

Basic information

Region (hg38): 15:83447227-83618743

Links

ENSG00000140600 ∙ NCBI:6457 ∙ OMIM:603362 ∙ HGNC:10832 ∙ Uniprot:Q99963 ∙ 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 SH3GL3 gene.

• Inborn genetic diseases (10 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SH3GL3 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						0
missense			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in SH3GL3

This is a list of pathogenic ClinVar variants found in the SH3GL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-83559296-A-G		not specified	Uncertain significance (Sep 14, 2023)
15-83559298-G-A		not specified	Uncertain significance (Jan 19, 2024)
15-83565138-T-C		not specified	Uncertain significance (Sep 13, 2023)
15-83568582-G-T		not specified	Uncertain significance (Apr 12, 2022)
15-83568655-G-A		not specified	Uncertain significance (Dec 21, 2023)
15-83572643-A-T		not specified	Uncertain significance (Jan 26, 2022)
15-83576674-C-T		not specified	Uncertain significance (Jul 12, 2022)
15-83587025-T-A		not specified	Uncertain significance (Mar 20, 2023)
15-83588697-A-G		not specified	Uncertain significance (Sep 16, 2021)
15-83588724-C-G		not specified	Uncertain significance (Aug 12, 2021)
15-83618087-A-G		not specified	Uncertain significance (May 22, 2023)
15-83618217-G-A			Uncertain significance (Oct 01, 2018)
15-83618221-G-T		not specified	Uncertain significance (Nov 18, 2022)
15-83618270-G-T		not specified	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SH3GL3	protein_coding	protein_coding	ENST00000427482	9	171516

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000102	0.988	125707	0	41	125748	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	138	184	0.750	0.00000975	2270
Missense in Polyphen		64	89.281	0.71684		1083
Synonymous	-0.762	79	70.8	1.12	0.00000431	630
Loss of Function	2.24	10	21.1	0.474	0.00000125	248

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000423	0.000416
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000163	0.000158
Middle Eastern	0.000163	0.000163
South Asian	0.000200	0.000196
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Implicated in endocytosis. May recruit other proteins to membranes with high curvature (By similarity). {ECO:0000250}.
• Pathway: Endocytosis - Homo sapiens (human);EGF-EGFR Signaling Pathway;Disease;Signal Transduction;Vesicle-mediated transport;Membrane Trafficking;Infectious disease;EGFR downregulation;Signaling by EGFR;Clathrin-mediated endocytosis;EGFR1;Cargo recognition for clathrin-mediated endocytosis;Negative regulation of MET activity;Signaling by MET;Signaling by Receptor Tyrosine Kinases;InlB-mediated entry of Listeria monocytogenes into host cell;Listeria monocytogenes entry into host cells (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.660
• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.27

Haploinsufficiency Scores

• pHI: 0.0858
• hipred: Y
• hipred_score: 0.714
• ghis: 0.437

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.860

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sh3gl3
• Phenotype: normal phenotype; 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system 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); growth/size/body region phenotype

Zebrafish Information Network

• Gene name: sh3gl3b
• Affected structure: blood cell
• Phenotype tag: abnormal
• Phenotype quality: accumulation

Gene ontology

• Biological process: endocytosis;signal transduction;central nervous system development;positive regulation of neuron differentiation;negative regulation of clathrin-dependent endocytosis
• Cellular component: acrosomal vesicle;early endosome membrane;presynapse;postsynaptic endosome;glutamatergic synapse;postsynaptic density, intracellular component
• Molecular function: protein binding;protein C-terminus binding;lipid binding;identical protein binding