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.

not_specified (32 variants)
not_provided (2 variants)

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. These statistics are base on transcript: NM_000032214.4. 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				2 clinvar		2
missense			29 clinvar	1 clinvar	2 clinvar	32
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	29	3	2

Loading clinvar variants...

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