SKAP1

src kinase associated phosphoprotein 1, the group of Pleckstrin homology domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 17:48133437-48430275

Previous symbols: [ "SCAP1" ]

Links

ENSG00000141293 ∙ NCBI:8631 ∙ OMIM:604969 ∙ HGNC:15605 ∙ Uniprot:Q86WV1 ∙ 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 SKAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SKAP1 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			20			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	20	0	0

Variants in SKAP1

This is a list of pathogenic ClinVar variants found in the SKAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-48137250-C-T		not specified	Uncertain significance (Jul 14, 2022)
17-48137296-G-C		not specified	Uncertain significance (Jan 11, 2023)
17-48162482-C-T		not specified	Uncertain significance (Dec 07, 2023)
17-48162495-C-T		not specified	Uncertain significance (Nov 12, 2021)
17-48162497-C-T		not specified	Uncertain significance (Sep 20, 2023)
17-48162516-C-T		not specified	Uncertain significance (Oct 26, 2022)
17-48180162-A-C		not specified	Uncertain significance (Mar 01, 2024)
17-48182405-A-G		not specified	Uncertain significance (Oct 06, 2021)
17-48182407-A-C		not specified	Uncertain significance (Jan 23, 2024)
17-48184748-G-A		not specified	Uncertain significance (Aug 08, 2023)
17-48184775-G-A		not specified	Uncertain significance (May 11, 2022)
17-48184832-C-T		not specified	Uncertain significance (Jan 26, 2022)
17-48187857-T-C		not specified	Uncertain significance (Jun 07, 2024)
17-48187908-G-A		not specified	Uncertain significance (Jul 20, 2021)
17-48345935-C-T		not specified	Uncertain significance (Apr 27, 2022)
17-48345938-C-T		not specified	Uncertain significance (Apr 05, 2023)
17-48345990-C-A		not specified	Uncertain significance (Apr 07, 2022)
17-48345997-A-G		not specified	Uncertain significance (Apr 18, 2023)
17-48345997-A-T		not specified	Uncertain significance (Dec 22, 2023)
17-48363802-A-C		not specified	Uncertain significance (Dec 14, 2023)
17-48396755-C-T		not specified	Uncertain significance (Apr 04, 2024)
17-48430093-T-A		not specified	Uncertain significance (Oct 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SKAP1	protein_coding	protein_coding	ENST00000336915	12	296836

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.82e-7	0.967	125725	0	21	125746	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.786	160	191	0.840	0.00000990	2377
Missense in Polyphen		42	60.1	0.69884		774
Synonymous	1.05	56	67.0	0.836	0.00000346	621
Loss of Function	2.04	15	26.3	0.571	0.00000145	300

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000959	0.0000959
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000547	0.0000544
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.0000972	0.0000967
Middle Eastern	0.0000547	0.0000544
South Asian	0.000133	0.000131
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Positively regulates T-cell receptor signaling by enhancing the MAP kinase pathway. Required for optimal conjugation between T-cells and antigen-presenting cells by promoting the clustering of integrin ITGAL on the surface of T-cells. May be involved in high affinity immunoglobulin epsilon receptor signaling in mast cells. {ECO:0000269|PubMed:10856234, ECO:0000269|PubMed:11909961, ECO:0000269|PubMed:12652296, ECO:0000269|PubMed:15939789, ECO:0000269|PubMed:16980616}.
• Pathway: Rap1 signaling pathway - Homo sapiens (human);T-Cell antigen Receptor (TCR) Signaling Pathway;TCR (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.783
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.76

Haploinsufficiency Scores

• pHI: 0.144
• hipred: Y
• hipred_score: 0.603
• ghis: 0.512

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.969

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Skap1
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: microtubule cytoskeleton organization;positive regulation of cell-matrix adhesion;adaptive immune response;positive regulation of adaptive immune response;positive regulation of signal transduction;cell migration;positive regulation of integrin activation;positive regulation of cell-cell adhesion mediated by integrin;positive regulation of heterotypic cell-cell adhesion;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;T cell receptor signaling pathway;cellular response to epidermal growth factor stimulus;protein localization to plasma membrane;positive regulation of leukocyte cell-cell adhesion
• Cellular component: ruffle;immunological synapse;nucleus;cytoplasm;cytosol;plasma membrane;cell-cell junction;microtubule plus-end;T cell receptor complex;plasma membrane raft
• Molecular function: SH3/SH2 adaptor activity;protein binding;SH3 domain binding;protein kinase binding;protein phosphatase binding;SH2 domain binding;protein homodimerization activity;protein-containing complex binding;microtubule plus-end binding