SLA

Src like adaptor, the group of SH2 domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 8:133036728-133102912

Links

ENSG00000155926NCBI:6503OMIM:601099HGNC:10902Uniprot:Q13239AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLA gene.

  • not_provided (65 variants)
  • not_specified (39 variants)
  • Inborn_genetic_diseases (21 variants)
  • Iodotyrosyl_coupling_defect (11 variants)
  • TG-related_disorder (2 variants)
  • Autoimmune_thyroid_disease,_susceptibility_to,_3 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLA gene is commonly pathogenic or not. These statistics are base on transcript: NM_001045556.3. 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
missense
28
clinvar
2
clinvar
30
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 28 3 0

Highest pathogenic variant AF is 0.0000712454

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SLAprotein_codingprotein_codingENST00000427060 766326
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.3430.656125735081257430.0000318
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.8761501830.8180.00001032026
Missense in Polyphen5990.770.64999994
Synonymous0.1587677.80.9770.00000477646
Loss of Function2.98417.50.2290.00000103175

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00005980.0000598
Ashkenazi Jewish0.0001980.000198
East Asian0.0001150.000109
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.0001150.000109
South Asian0.00006540.0000653
Other0.000.00

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. Involved in the negative regulation of positive selection and mitosis of 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:10449770, ECO:0000269|PubMed:11696592}.;
Pathway
TCR;PDGFR-beta signaling pathway (Consensus)

Recessive Scores

pRec
0.329

Intolerance Scores

loftool
0.168
rvis_EVS
-0.09
rvis_percentile_EVS
46.74

Haploinsufficiency Scores

pHI
0.642
hipred
Y
hipred_score
0.776
ghis
0.550

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.866

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sla
Phenotype
cellular phenotype; immune system phenotype; hematopoietic system phenotype;

Gene ontology

Biological process
positive regulation of signal transduction;cell differentiation;peptidyl-tyrosine autophosphorylation;regulation of cell population proliferation
Cellular component
endosome
Molecular function
non-membrane spanning protein tyrosine kinase activity;SH3/SH2 adaptor activity;protein binding