SLA2

Src like adaptor 2, the group of SH2 domain containing

Basic information

Region (hg38): 20:36612318-36646196

Previous symbols: [ "C20orf156" ]

Links

ENSG00000101082NCBI:84174OMIM:606577HGNC:17329Uniprot:Q9H6Q3AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
2
clinvar
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)3162699
20-36614342-C-T Benign (Jun 27, 2018)781498
20-36614359-A-G not specified Uncertain significance (Jun 17, 2024)3318757
20-36614396-C-T not specified Uncertain significance (Aug 30, 2021)2247227
20-36615252-G-A not specified Uncertain significance (Jun 07, 2023)2558484
20-36615326-C-T not specified Uncertain significance (Jul 25, 2023)2588442
20-36615327-G-C not specified Uncertain significance (Jan 10, 2022)2271718
20-36615353-C-T not specified Uncertain significance (Nov 30, 2022)2359305
20-36615354-G-A not specified Uncertain significance (Mar 11, 2024)3162698
20-36615365-G-C not specified Uncertain significance (Nov 15, 2024)3442397
20-36632603-G-A not specified Uncertain significance (Jul 20, 2021)2341999
20-36632637-G-C not specified Uncertain significance (Dec 20, 2022)2219565
20-36632646-G-A not specified Uncertain significance (Jun 11, 2024)3318756
20-36633606-A-G not specified Uncertain significance (Oct 05, 2023)3162697
20-36633612-G-A not specified Uncertain significance (Nov 13, 2024)3442400
20-36633612-G-C not specified Uncertain significance (Nov 14, 2023)3162696
20-36634526-G-A not specified Uncertain significance (Jun 28, 2024)3442398
20-36634550-G-A Benign (Jul 21, 2018)781751
20-36634577-G-A not specified Uncertain significance (Mar 10, 2025)3796333
20-36641268-T-G not specified Uncertain significance (Oct 29, 2024)3442399
20-36641283-G-A not specified Uncertain significance (Feb 28, 2023)2491499
20-36641307-G-T not specified Uncertain significance (Aug 09, 2021)2241504
20-36641316-C-A not specified Uncertain significance (Aug 28, 2024)3442396

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SLA2protein_codingprotein_codingENST00000262866 733899
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.07630.9131257261201257470.0000835
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.1021471510.9770.000008471663
Missense in Polyphen4759.7240.78696628
Synonymous-0.09306867.01.010.00000407555
Loss of Function2.24412.60.3195.30e-7154

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002030.000203
Ashkenazi Jewish0.00009930.0000992
East Asian0.0002740.000272
Finnish0.000.00
European (Non-Finnish)0.00003520.0000352
Middle Eastern0.0002740.000272
South Asian0.0001310.0000980
Other0.0001630.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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