SLA

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

Basic information

Region (hg38): 8:133036728-133102912

Links

ENSG00000155926

∙ NCBI:6503 ∙ OMIM:601099 ∙ HGNC:10902 ∙ Uniprot:Q13239 ∙ 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 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
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

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLA	protein_coding	protein_coding	ENST00000427060	7	66326

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.343	0.656	125735	0	8	125743	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.876	150	183	0.818	0.0000103	2026
Missense in Polyphen		59	90.77	0.64999		994
Synonymous	0.158	76	77.8	0.977	0.00000477	646
Loss of Function	2.98	4	17.5	0.229	0.00000103	175

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000598	0.0000598
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000115	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000115	0.000109
South Asian	0.0000654	0.0000653
Other	0.00	0.00

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

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

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