SLA2

Src like adaptor 2, the group of SH2 domain containing

Basic information

Region (hg38): 20:36612318-36646196

Previous symbols: [ "C20orf156" ]

Links

ENSG00000101082 ∙ NCBI:84174 ∙ OMIM:606577 ∙ HGNC:17329 ∙ Uniprot:Q9H6Q3 ∙ 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 SLA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLA2 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		2	22
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	2

Variants in SLA2

This is a list of pathogenic ClinVar variants found in the SLA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-36613907-T-C		not specified	Uncertain significance (Dec 19, 2023)
20-36614342-C-T			Benign (Jun 27, 2018)
20-36614359-A-G		not specified	Uncertain significance (Jun 17, 2024)
20-36614396-C-T		not specified	Uncertain significance (Aug 30, 2021)
20-36615252-G-A		not specified	Uncertain significance (Jun 07, 2023)
20-36615326-C-T		not specified	Uncertain significance (Jul 25, 2023)
20-36615327-G-C		not specified	Uncertain significance (Jan 10, 2022)
20-36615353-C-T		not specified	Uncertain significance (Nov 30, 2022)
20-36615354-G-A		not specified	Uncertain significance (Mar 11, 2024)
20-36615365-G-C		not specified	Uncertain significance (Nov 15, 2024)
20-36632603-G-A		not specified	Uncertain significance (Jul 20, 2021)
20-36632637-G-C		not specified	Uncertain significance (Dec 20, 2022)
20-36632646-G-A		not specified	Uncertain significance (Jun 11, 2024)
20-36633606-A-G		not specified	Uncertain significance (Oct 05, 2023)
20-36633612-G-A		not specified	Uncertain significance (Nov 13, 2024)
20-36633612-G-C		not specified	Uncertain significance (Nov 14, 2023)
20-36634526-G-A		not specified	Uncertain significance (Jun 28, 2024)
20-36634550-G-A			Benign (Jul 21, 2018)
20-36634577-G-A		not specified	Uncertain significance (Mar 10, 2025)
20-36641268-T-G		not specified	Uncertain significance (Oct 29, 2024)
20-36641283-G-A		not specified	Uncertain significance (Feb 28, 2023)
20-36641307-G-T		not specified	Uncertain significance (Aug 09, 2021)
20-36641316-C-A		not specified	Uncertain significance (Aug 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLA2	protein_coding	protein_coding	ENST00000262866	7	33899

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0763	0.913	125726	1	20	125747	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.102	147	151	0.977	0.00000847	1663
Missense in Polyphen		47	59.724	0.78696		628
Synonymous	-0.0930	68	67.0	1.01	0.00000407	555
Loss of Function	2.24	4	12.6	0.319	5.30e-7	154

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000203	0.000203
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000274	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.000274	0.000272
South Asian	0.000131	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Adapter protein, which negatively regulates T-cell receptor (TCR) signaling. Inhibits T-cell antigen-receptor induced activation of nuclear factor of activated T-cells. May act by linking signaling proteins such as ZAP70 with CBL, leading to a CBL dependent degradation of signaling proteins. {ECO:0000269|PubMed:11696592}.
• Pathway: TCR;BCR;TCR signaling in naïve CD4+ T cells (Consensus)

Recessive Scores

• pRec: 0.234

Intolerance Scores

• loftool: 0.260
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.26

Haploinsufficiency Scores

• pHI: 0.0979
• hipred: Y
• hipred_score: 0.681
• ghis: 0.429

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.685

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sla2
• Phenotype: cellular phenotype; immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;positive regulation of signal transduction;B cell mediated immunity;intracellular receptor signaling pathway;T cell activation;regulation of phosphatidylinositol 3-kinase activity;negative regulation of insulin receptor signaling pathway;phosphatidylinositol phosphorylation;regulation of immune response;negative regulation of calcium-mediated signaling;antigen receptor-mediated signaling pathway;negative regulation of B cell activation
• Cellular component: nucleoplasm;cytoplasm;late endosome;Golgi apparatus;plasma membrane;phosphatidylinositol 3-kinase complex;endosome membrane;intracellular membrane-bounded organelle
• Molecular function: SH3/SH2 adaptor activity;protein binding;1-phosphatidylinositol-3-kinase regulator activity;protein N-terminus binding