SLA

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

Basic information

Region (hg38): 8:133036727-133102912

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 (31 variants)
• Inborn genetic diseases (25 variants)
• Iodotyrosyl coupling defect (13 variants)
• not specified (4 variants)
• Iodotyrosyl coupling defect;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.

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			13	2		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	2		18	13	8	41
Total	2	0	31	15	8

Variants in SLA

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

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

Position	Type	Phenotype	Significance	ClinVar
8-133038561-C-T		not specified	Uncertain significance (Jul 27, 2022)
8-133038609-C-T		not specified	Uncertain significance (Jun 11, 2021)
8-133038655-C-T		not specified	Uncertain significance (Mar 29, 2022)
8-133038666-C-T		not specified	Uncertain significance (Sep 12, 2023)
8-133038691-C-T		not specified	Uncertain significance (May 24, 2023)
8-133040106-A-C		not specified	Uncertain significance (Jul 09, 2021)
8-133040109-C-T		not specified	Uncertain significance (Mar 30, 2022)
8-133047916-A-G		not specified	Uncertain significance (Jun 27, 2022)
8-133050846-C-T		not specified	Uncertain significance (Jun 01, 2023)
8-133050847-G-A		not specified	Uncertain significance (Nov 13, 2023)
8-133050859-G-A		not specified	Uncertain significance (Mar 13, 2023)
8-133050875-C-T		not specified	Likely benign (Jan 08, 2024)
8-133050904-C-T		not specified	Uncertain significance (Feb 03, 2022)
8-133050908-A-C		not specified	Likely benign (Oct 27, 2023)
8-133050908-A-T		not specified	Likely benign (Jun 02, 2023)
8-133060107-G-T		not specified	Uncertain significance (Jan 18, 2022)
8-133060180-G-A		not specified	Uncertain significance (Nov 08, 2022)
8-133060220-C-T		not specified	Uncertain significance (Apr 28, 2022)
8-133060235-G-A		not specified	Likely benign (Oct 12, 2021)
8-133094892-T-G			Benign (Jun 19, 2021)
8-133094979-A-G			Benign (Jun 19, 2021)
8-133095033-T-G			Likely benign (Oct 23, 2023)
8-133095035-C-G			Likely benign (Jan 20, 2024)
8-133095052-C-T		Iodotyrosyl coupling defect	Conflicting classifications of pathogenicity (Nov 01, 2023)
8-133095053-G-A			Likely benign (Feb 01, 2023)

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