SH3GL1

SH3 domain containing GRB2 like 1, endophilin A2, the group of N-BAR domain containing

Basic information

Region (hg38): 19:4360370-4400547

Links

ENSG00000141985 ∙ NCBI:6455 ∙ OMIM:601768 ∙ HGNC:10830 ∙ Uniprot:Q99961 ∙ 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 SH3GL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SH3GL1 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				1	3	4
missense			23	1		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					6	6
Total	0	0	23	2	9

Variants in SH3GL1

This is a list of pathogenic ClinVar variants found in the SH3GL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-4361606-C-T		not specified	Likely benign (Sep 11, 2024)
19-4361642-G-A			Benign (Oct 19, 2017)
19-4361706-G-A		not specified	Uncertain significance (Jun 03, 2024)
19-4361713-C-T		not specified	Likely benign (Nov 21, 2022)
19-4361740-C-T		not specified	Uncertain significance (Jun 07, 2023)
19-4361755-C-G		not specified	Uncertain significance (Dec 13, 2021)
19-4361994-GTT-G			Benign (Nov 12, 2018)
19-4362338-G-A		not specified	Uncertain significance (May 27, 2022)
19-4362349-C-T		not specified	Uncertain significance (May 26, 2022)
19-4362362-C-T		not specified	Uncertain significance (Feb 28, 2023)
19-4362370-C-G		not specified	Uncertain significance (Aug 08, 2022)
19-4362370-C-T		not specified	Uncertain significance (May 31, 2023)
19-4362620-T-C		not specified	Uncertain significance (Jun 16, 2023)
19-4362627-C-T		not specified	Uncertain significance (Mar 01, 2023)
19-4362655-C-G		not specified	Uncertain significance (Sep 20, 2023)
19-4362687-G-A		not specified	Uncertain significance (Dec 17, 2023)
19-4362694-G-C		Acute myeloid leukemia	Benign (Jul 15, 2021)
19-4362707-C-T		not specified	Uncertain significance (Apr 12, 2024)
19-4362735-T-A		not specified	Uncertain significance (Jun 24, 2022)
19-4363173-G-T			Benign (Nov 12, 2018)
19-4363292-C-T			Benign (Jun 19, 2021)
19-4363374-G-A		not specified	Uncertain significance (Mar 08, 2024)
19-4363410-C-T		not specified	Uncertain significance (Apr 13, 2022)
19-4363416-G-C		not specified	Uncertain significance (Jan 23, 2024)
19-4363418-C-T		not specified	Uncertain significance (Jun 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SH3GL1	protein_coding	protein_coding	ENST00000269886	10	40178

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0117	0.987	125712	0	17	125729	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.918	195	235	0.831	0.0000170	2391
Missense in Polyphen		37	63.344	0.58411		681
Synonymous	-3.26	155	111	1.39	0.00000895	701
Loss of Function	2.77	7	20.6	0.340	0.00000111	231

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000285	0.000277
European (Non-Finnish)	0.0000629	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000666	0.0000653
Other	0.000168	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Implicated in endocytosis. May recruit other proteins to membranes with high curvature (By similarity). {ECO:0000250}.
• Disease: DISEASE: Note=In some cases of acute leukemia, a translocation results in the formation of a KMT2A/MLL1-EEN fusion gene. {ECO:0000269|PubMed:9122235}.
• Pathway: Endocytosis - Homo sapiens (human);Disease;Signal Transduction;Vesicle-mediated transport;Membrane Trafficking;Infectious disease;EGFR downregulation;Signaling by EGFR;Clathrin-mediated endocytosis;Cargo recognition for clathrin-mediated endocytosis;Negative regulation of MET activity;Signaling by MET;Signaling by Receptor Tyrosine Kinases;Signaling events mediated by focal adhesion kinase;InlB-mediated entry of Listeria monocytogenes into host cell;Listeria monocytogenes entry into host cells (Consensus)

Intolerance Scores

• loftool: 0.292
• rvis_EVS: -1.02
• rvis_percentile_EVS: 8

Haploinsufficiency Scores

• pHI: 0.0687
• hipred: Y
• hipred_score: 0.756
• ghis: 0.588

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.907

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sh3gl1
• 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); respiratory system 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); growth/size/body region phenotype

Gene ontology

• Biological process: signal transduction;central nervous system development;synaptic vesicle uncoating;modulation of excitatory postsynaptic potential;positive regulation of synaptic vesicle endocytosis
• Cellular component: podosome;cytoplasm;cytosol;cell junction;early endosome membrane;cell projection;Schaffer collateral - CA1 synapse;hippocampal mossy fiber to CA3 synapse;presynapse;glutamatergic synapse;postsynaptic density, intracellular component
• Molecular function: protein binding;protein C-terminus binding;lipid binding;SH3 domain binding;phosphatase binding;beta-1 adrenergic receptor binding;identical protein binding;ion channel binding;cadherin binding;GTPase binding