STAC

SH3 and cysteine rich domain

Basic information

Region (hg38): 3:36380502-36548007

Links

ENSG00000144681 ∙ NCBI:6769 ∙ OMIM:602317 ∙ HGNC:11353 ∙ Uniprot:Q99469 ∙ 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 STAC gene.

• Inborn genetic diseases (18 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STAC 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			18		2	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	2

Variants in STAC

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

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

Position	Type	Phenotype	Significance	ClinVar
3-36380681-A-C			Benign (Dec 31, 2019)
3-36380710-G-C		not specified	Uncertain significance (Jun 12, 2023)
3-36443410-G-A		not specified	Uncertain significance (Jun 21, 2023)
3-36443436-C-A		not specified	Uncertain significance (Jun 26, 2023)
3-36443440-G-A		not specified	Uncertain significance (Dec 19, 2022)
3-36443458-T-G		not specified	Uncertain significance (Mar 02, 2023)
3-36443481-G-A		not specified	Uncertain significance (Apr 06, 2023)
3-36443560-C-T		not specified	Uncertain significance (Feb 15, 2023)
3-36443616-G-A		not specified	Uncertain significance (Dec 19, 2022)
3-36483015-C-T		not specified	Uncertain significance (Jul 14, 2022)
3-36483045-C-T		not specified	Uncertain significance (Mar 20, 2023)
3-36484990-G-A		not specified	Uncertain significance (Nov 21, 2023)
3-36486163-G-C		not specified	Uncertain significance (Oct 18, 2021)
3-36486191-C-T		not specified	Uncertain significance (Dec 28, 2022)
3-36486217-G-A		not specified	Uncertain significance (Aug 12, 2021)
3-36504411-A-G			Benign (Mar 29, 2018)
3-36504438-C-T		not specified	Uncertain significance (Sep 01, 2021)
3-36505774-T-C		not specified	Uncertain significance (May 08, 2023)
3-36505806-C-T		not specified	Uncertain significance (Nov 30, 2021)
3-36528873-T-C		not specified	Uncertain significance (Apr 07, 2023)
3-36546284-A-C		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STAC	protein_coding	protein_coding	ENST00000273183	11	167664

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.44e-7	0.839	125662	1	85	125748	0.000342

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.304	209	222	0.943	0.0000117	2657
Missense in Polyphen		78	86.393	0.90285		1043
Synonymous	-1.51	98	80.8	1.21	0.00000424	734
Loss of Function	1.52	14	21.6	0.648	0.00000110	255

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000576	0.000571
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00185	0.00180
European (Non-Finnish)	0.000186	0.000185
Middle Eastern	0.000218	0.000217
South Asian	0.0000992	0.0000980
Other	0.000497	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes expression of the ion channel CACNA1H at the cell membrane, and thereby contributes to the regulation of channel activity. Plays a minor and redundant role in promoting the expression of calcium channel CACNA1S at the cell membrane, and thereby contributes to increased channel activity. Slows down the inactivation rate of the calcium channel CACNA1C. {ECO:0000250|UniProtKB:P97306}.

Recessive Scores

• pRec: 0.0931

Intolerance Scores

• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.45

Haploinsufficiency Scores

• pHI: 0.418
• hipred: N
• hipred_score: 0.492
• ghis: 0.464

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.197

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stac

Gene ontology

• Biological process: muscle contraction;signal transduction;cellular response to heat;intracellular signal transduction;positive regulation of voltage-gated calcium channel activity;positive regulation of protein localization to plasma membrane;positive regulation of cation channel activity
• Cellular component: cytosol;T-tubule;extrinsic component of cytoplasmic side of plasma membrane
• Molecular function: protein binding;ion channel binding;metal ion binding