SH3TC1

SH3 domain and tetratricopeptide repeats 1, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 4:8182072-8241803

Links

ENSG00000125089 ∙ NCBI:54436 ∙ ∙ HGNC:26009 ∙ Uniprot:Q8TE82 ∙ 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 SH3TC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SH3TC1 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				9	2	11
missense			137	10		147
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	137	19	3

Variants in SH3TC1

This is a list of pathogenic ClinVar variants found in the SH3TC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-8205207-C-T		not specified	Uncertain significance (Dec 18, 2023)
4-8205252-G-T		not specified	Uncertain significance (Apr 15, 2024)
4-8205279-C-T		not specified	Uncertain significance (Dec 17, 2021)
4-8205303-A-T		not specified	Uncertain significance (Apr 23, 2024)
4-8205352-C-T		not specified	Uncertain significance (Apr 07, 2022)
4-8205583-G-A			Likely benign (Jan 01, 2023)
4-8209749-C-A		not specified	Uncertain significance (Oct 26, 2021)
4-8209753-G-A		not specified	Uncertain significance (Sep 26, 2022)
4-8209765-C-T		not specified	Uncertain significance (Nov 26, 2024)
4-8209810-G-T		not specified	Uncertain significance (Mar 28, 2023)
4-8212702-C-A		not specified	Uncertain significance (Sep 16, 2021)
4-8212724-G-A		not specified	Uncertain significance (Dec 06, 2023)
4-8212727-C-T		not specified	Uncertain significance (Oct 20, 2023)
4-8212741-A-C		not specified	Uncertain significance (Sep 02, 2024)
4-8212769-C-T		not specified	Uncertain significance (Aug 30, 2022)
4-8212773-G-A		not specified	Uncertain significance (Dec 03, 2024)
4-8212818-G-A		not specified	Uncertain significance (Jun 12, 2023)
4-8212820-G-A		not specified	Uncertain significance (Dec 13, 2022)
4-8214512-A-G		not specified	Uncertain significance (Mar 15, 2024)
4-8214517-C-T		not specified	Uncertain significance (Aug 17, 2021)
4-8214523-G-A		not specified	Uncertain significance (Nov 29, 2023)
4-8214539-C-A		not specified	Uncertain significance (Nov 20, 2023)
4-8214563-C-T		not specified	Uncertain significance (Nov 27, 2024)
4-8214572-A-T		not specified	Uncertain significance (Oct 26, 2021)
4-8216131-G-A		not specified	Uncertain significance (Apr 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SH3TC1	protein_coding	protein_coding	ENST00000245105	17	59732

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.09e-35	0.00000872	123993	13	1741	125747	0.00700

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.15	982	810	1.21	0.0000542	8455
Missense in Polyphen		293	243.96	1.201		2936
Synonymous	-2.38	444	385	1.15	0.0000277	2857
Loss of Function	-0.0858	52	51.3	1.01	0.00000254	577

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0144	0.0141
Ashkenazi Jewish	0.0166	0.0157
East Asian	0.00377	0.00370
Finnish	0.00113	0.00111
European (Non-Finnish)	0.00718	0.00695
Middle Eastern	0.00377	0.00370
South Asian	0.0114	0.0107
Other	0.00824	0.00768

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.882
• rvis_EVS: 1.02
• rvis_percentile_EVS: 90.88

Haploinsufficiency Scores

• pHI: 0.0674
• hipred: N
• hipred_score: 0.170
• ghis: 0.485

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.546

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sh3tc1

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component