STAP1

signal transducing adaptor family member 1, the group of SH2 domain containing

Basic information

Region (hg38): 4:67558726-67607337

Links

ENSG00000035720 ∙ NCBI:26228 ∙ OMIM:604298 ∙ HGNC:24133 ∙ Uniprot:Q9ULZ2 ∙ 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 STAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STAP1 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				26	2	28
missense		1	57	2	1	61
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				7	12	19
Total	0	1	57	35	15

Variants in STAP1

This is a list of pathogenic ClinVar variants found in the STAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-67558807-G-T		STAP1-related disorder	Likely benign (Nov 30, 2020)
4-67558814-T-C		STAP1-related disorder	Benign (Feb 20, 2019)
4-67558823-A-G		not specified	Uncertain significance (May 22, 2023)
4-67558828-C-A		not specified	Uncertain significance (May 08, 2023)
4-67558843-C-G		not specified	Uncertain significance (Aug 07, 2021)
4-67558851-C-A		not specified	Likely benign (Aug 24, 2019)
4-67558859-A-G		not specified	Uncertain significance (Feb 02, 2022)
4-67558866-A-G		not specified	Likely benign (Nov 08, 2023)
4-67558877-C-T			Uncertain significance (-)
4-67558895-A-C		not specified	Uncertain significance (Feb 06, 2024)
4-67558915-C-T		not specified	Uncertain significance (Mar 21, 2022)
4-67558916-G-A		not specified	Uncertain significance (Jun 09, 2024)
4-67558922-G-C		not specified	Uncertain significance (Oct 09, 2022)
4-67558927-C-T		not specified	Uncertain significance (Dec 04, 2022)
4-67558928-G-A		not specified	Likely benign (Jul 12, 2021)
4-67558935-T-C		STAP1-related disorder	Benign/Likely benign (Aug 07, 2020)
4-67570858-T-C			Benign (Sep 21, 2018)
4-67570978-C-T			Likely benign (Sep 29, 2018)
4-67571090-G-A		not specified	Likely benign (Aug 10, 2021)
4-67571102-A-G		Hypercholesterolemia, familial, 1	Likely pathogenic (-)
4-67571107-G-A		not specified	Likely benign (Jul 19, 2020)
4-67571108-T-C		not specified	Likely benign (Nov 17, 2022)
4-67571117-A-G		not specified	Uncertain significance (Oct 05, 2023)
4-67571120-A-C		not specified	Uncertain significance (Mar 08, 2024)
4-67571121-C-T		not specified	Uncertain significance (May 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STAP1	protein_coding	protein_coding	ENST00000265404	9	48610

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000170	0.885	125708	0	39	125747	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0251	155	156	0.994	0.00000816	1932
Missense in Polyphen		35	46.265	0.75651		546
Synonymous	-1.16	64	53.3	1.20	0.00000278	523
Loss of Function	1.50	10	16.6	0.602	8.56e-7	218

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000522	0.000521
Ashkenazi Jewish	0.00	0.00
East Asian	0.000219	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000196	0.000193
Middle Eastern	0.000219	0.000217
South Asian	0.00	0.00
Other	0.000344	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: In BCR signaling, appears to function as a docking protein acting downstream of TEC and participates in a positive feedback loop by increasing the activity of TEC. {ECO:0000269|PubMed:10518561}.
• Pathway: BCR;Signaling events mediated by Stem cell factor receptor (c-Kit) (Consensus)

Recessive Scores

• pRec: 0.0976

Intolerance Scores

• loftool: 0.563
• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.44

Haploinsufficiency Scores

• pHI: 0.663
• hipred: N
• hipred_score: 0.245
• ghis: 0.634

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.760

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stap1

Gene ontology

• Biological process: transmembrane receptor protein tyrosine kinase signaling pathway;positive regulation of gene expression;negative regulation of macrophage chemotaxis;negative regulation of phosphorylation;positive regulation of B cell receptor signaling pathway;positive regulation of phagocytosis, engulfment;cellular response to lipopolysaccharide;negative regulation of ruffle assembly;negative regulation of macrophage colony-stimulating factor signaling pathway;positive regulation of microglial cell activation;positive regulation of non-membrane spanning protein tyrosine kinase activity;negative regulation of microglial cell migration;positive regulation of microglial cell mediated cytotoxicity;positive regulation of actin cytoskeleton reorganization
• Cellular component: nucleus;nucleoplasm;cytoplasm;mitochondrion;protein-containing complex;intracellular membrane-bounded organelle
• Molecular function: phosphotyrosine residue binding;transmembrane receptor protein tyrosine kinase adaptor activity;SH3/SH2 adaptor activity;macrophage colony-stimulating factor receptor binding;protein binding;phospholipid binding;protein kinase binding