STAC2

SH3 and cysteine rich domain 2

Basic information

Region (hg38): 17:39210541-39225945

Links

ENSG00000141750 ∙ NCBI:342667 ∙ ∙ HGNC:23990 ∙ Uniprot:Q6ZMT1 ∙ 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 STAC2 gene.

• not_specified (59 variants)
• not_provided (2 variants)
• High_myopia (1 variants)
• Childhood-onset_schizophrenia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STAC2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000198993.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense		1	60			61
nonsense						0
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)						0
Total	0	1	61	0	0

Highest pathogenic variant AF is 0.000002164699

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STAC2	protein_coding	protein_coding	ENST00000333461	11	15337

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.41e-7	0.921	125693	0	55	125748	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0999	251	247	1.02	0.0000145	2645
Missense in Polyphen		77	80.286	0.95907		798
Synonymous	-0.242	99	96.0	1.03	0.00000531	807
Loss of Function	1.73	13	21.7	0.599	0.00000110	224

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000680	0.000668
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.0000547	0.0000544
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.000296	0.000290
Middle Eastern	0.0000547	0.0000544
South Asian	0.000134	0.000131
Other	0.000169	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a 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:Q8R1B0}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.397
• rvis_EVS: -0.98
• rvis_percentile_EVS: 8.8

Haploinsufficiency Scores

• pHI: 0.254
• hipred: N
• hipred_score: 0.205
• ghis: 0.529

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.164

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stac2

Gene ontology

• Biological process: intracellular signal transduction;positive regulation of voltage-gated calcium channel activity;positive regulation of protein localization to plasma membrane
• Cellular component: cytosol;extrinsic component of cytoplasmic side of plasma membrane;sarcolemma
• Molecular function: protein binding;metal ion binding