STAP1

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

Basic information

Region (hg38): 4:67558727-67607337

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.

not_specified (130 variants)
not_provided (8 variants)
STAP1-related_disorder (4 variants)
Hypercholesterolemia,_familial,_1 (1 variants)

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. These statistics are base on transcript: NM_000012108.4. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				38 clinvar		38
missense		1 clinvar	88 clinvar	5 clinvar	1 clinvar	95
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	1	88	43	1

Highest pathogenic variant AF is 0.0000055845053

Loading clinvar variants...

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
Phenotype

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