SH3GLB1

SH3 domain containing GRB2 like, endophilin B1, the group of N-BAR domain containing|Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 1:86704570-86748184

Links

ENSG00000097033 ∙ NCBI:51100 ∙ OMIM:609287 ∙ HGNC:10833 ∙ Uniprot:Q9Y371 ∙ 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 SH3GLB1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SH3GLB1 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			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	0

Variants in SH3GLB1

This is a list of pathogenic ClinVar variants found in the SH3GLB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-86704964-C-T		not specified	Uncertain significance (Jan 24, 2023)
1-86715783-C-A		not specified	Uncertain significance (Oct 14, 2023)
1-86715801-A-C		not specified	Uncertain significance (Sep 17, 2021)
1-86715803-G-A		not specified	Uncertain significance (Nov 18, 2023)
1-86715811-A-G		not specified	Uncertain significance (Aug 13, 2021)
1-86719507-A-G		not specified	Uncertain significance (Jan 26, 2022)
1-86719561-G-A		not specified	Uncertain significance (Feb 23, 2023)
1-86719585-G-A		not specified	Uncertain significance (Aug 17, 2022)
1-86719593-A-G		not specified	Uncertain significance (Apr 25, 2022)
1-86719606-G-C		not specified	Uncertain significance (May 02, 2024)
1-86722566-A-G		not specified	Uncertain significance (Aug 15, 2023)
1-86722632-C-A		not specified	Uncertain significance (Jul 31, 2024)
1-86722668-A-G		not specified	Uncertain significance (Oct 17, 2024)
1-86724368-G-A		not specified	Uncertain significance (Oct 10, 2023)
1-86728418-C-T		not specified	Uncertain significance (Aug 23, 2021)
1-86728419-G-A		not specified	Uncertain significance (Feb 13, 2025)
1-86728472-C-A		not specified	Uncertain significance (Oct 21, 2024)
1-86728472-C-T		not specified	Uncertain significance (Jan 16, 2025)
1-86728481-T-A		not specified	Uncertain significance (Nov 11, 2024)
1-86734677-A-G		not specified	Uncertain significance (Dec 13, 2023)
1-86734687-C-T		not specified	Uncertain significance (Mar 08, 2025)
1-86734690-A-G		not specified	Uncertain significance (Feb 14, 2023)
1-86735149-A-G		not specified	Uncertain significance (Jan 30, 2024)
1-86742219-A-G		not specified	Uncertain significance (Jan 02, 2024)
1-86742293-G-T		not specified	Uncertain significance (Nov 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SH3GLB1	protein_coding	protein_coding	ENST00000482504	11	43609

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.994	0.00593	125737	0	5	125742	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.63	130	194	0.671	0.00000914	2531
Missense in Polyphen		46	84.375	0.54518		1098
Synonymous	1.01	56	66.5	0.843	0.00000312	704
Loss of Function	3.90	1	19.7	0.0509	8.27e-7	278

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000647	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000604	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.0000604	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be required for normal outer mitochondrial membrane dynamics (PubMed:15452144). Required for coatomer-mediated retrograde transport in certain cells (By similarity). May recruit other proteins to membranes with high curvature. May promote membrane fusion (PubMed:11604418). Involved in activation of caspase-dependent apoptosis by promoting BAX/BAK1 activation (PubMed:16227588). Isoform 1 acts proapoptotic in fibroblasts (By similarity). Involved in caspase-independent apoptosis during nutrition starvation and involved in the regulation of autophagy. Activates lipid kinase activity of PIK3C3 during autophagy probably by associating with the PI3K complex II (PI3KC3-C2) (PubMed:17891140). Associated with PI3KC3-C2 during autophagy may regulate the trafficking of ATG9A from the Golgi complex to the peripheral cytoplasm for the formation of autophagosomes by inducing Golgi membrane tubulation and fragmentation (PubMed:21068542). Involved in regulation of degradative endocytic trafficking and cytokinesis, probably in the context of PI3KC3-C2 (PubMed:20643123). Isoform 2 acts antiapoptotic in neuronal cells; involved in maintenance of mitochondrial morphology and promotes neuronal viability (By similarity). {ECO:0000250|UniProtKB:Q9JK48, ECO:0000269|PubMed:11604418, ECO:0000269|PubMed:15452144, ECO:0000269|PubMed:17891140, ECO:0000269|PubMed:20643123, ECO:0000269|PubMed:21068542}.
• Pathway: Endocytosis - Homo sapiens (human);Autophagy - animal - Homo sapiens (human);Nanoparticle triggered autophagic cell death;Senescence and Autophagy in Cancer (Consensus)

Recessive Scores

• pRec: 0.131

Intolerance Scores

• loftool: 0.208
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.108
• hipred: Y
• hipred_score: 0.654
• ghis: 0.563

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.862

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sh3glb1
• Phenotype: cellular phenotype

Gene ontology

• Biological process: autophagy;apoptotic process;positive regulation of autophagy;regulation of macroautophagy;regulation of protein stability;positive regulation of protein oligomerization;regulation of cytokinesis;receptor catabolic process;cellular response to amino acid starvation;cellular response to glucose starvation;autophagic cell death;protein complex oligomerization;membrane fission;positive regulation of membrane tubulation;protein localization to vacuolar membrane;positive regulation of protein targeting to mitochondrion;positive regulation of autophagosome assembly
• Cellular component: Golgi membrane;autophagosome membrane;cytoplasm;mitochondrial outer membrane;cytosol;midbody;cytoplasmic vesicle
• Molecular function: protein binding;lipid binding;identical protein binding;protein homodimerization activity;cadherin binding