SKAP2

src kinase associated phosphoprotein 2, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 7:26667067-26995239

Previous symbols: [ "SCAP2" ]

Links

ENSG00000005020 ∙ NCBI:8935 ∙ OMIM:605215 ∙ HGNC:15687 ∙ Uniprot:O75563 ∙ 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 SKAP2 gene.

• Inborn genetic diseases (8 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SKAP2 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					1	1
missense			7	1	2	10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	3

Variants in SKAP2

This is a list of pathogenic ClinVar variants found in the SKAP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-26725466-C-G			Benign (Feb 26, 2018)
7-26725472-G-A		not specified	Uncertain significance (Jul 09, 2021)
7-26738871-G-A			Benign (Jul 16, 2018)
7-26739929-G-C		not specified	Uncertain significance (Nov 22, 2021)
7-26844099-C-A		not specified	Uncertain significance (Jul 05, 2023)
7-26844104-G-T		not specified	Uncertain significance (Oct 04, 2022)
7-26844125-T-G		not specified	Uncertain significance (Jun 22, 2021)
7-26854786-T-C		not specified	Likely benign (Feb 23, 2023)
7-26854811-A-C		not specified	Uncertain significance (Sep 17, 2021)
7-26864372-G-C		not specified	Uncertain significance (Aug 08, 2022)
7-26864395-G-A			Benign (Jun 11, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SKAP2	protein_coding	protein_coding	ENST00000345317	12	328178

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00128	0.997	125726	0	21	125747	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.30	133	182	0.730	0.00000857	2390
Missense in Polyphen		29	67.653	0.42866		912
Synonymous	-0.465	63	58.5	1.08	0.00000260	599
Loss of Function	2.76	9	23.4	0.384	0.00000106	305

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000153	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000707	0.0000703
Middle Eastern	0.000109	0.000109
South Asian	0.000203	0.000196
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in B-cell and macrophage adhesion processes. In B-cells, may act by coupling the B-cell receptor (BCR) to integrin activation. May play a role in src signaling pathway. {ECO:0000269|PubMed:12893833, ECO:0000269|PubMed:9837776}.
• Pathway: TCR;Signal regulatory protein family interactions;Cell-Cell communication (Consensus)

Recessive Scores

• pRec: 0.262

Intolerance Scores

• loftool: 0.509
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.76

Haploinsufficiency Scores

• pHI: 0.820
• hipred: Y
• hipred_score: 0.775
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.942

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Skap2
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype

Gene ontology

• Biological process: signal transduction;negative regulation of cell population proliferation;positive regulation of signal transduction;B cell activation;protein-containing complex assembly
• Cellular component: nucleoplasm;cytoplasm;cytosol;plasma membrane
• Molecular function: SH3/SH2 adaptor activity;protein binding