SLC50A1

solute carrier family 50 member 1, the group of Solute carrier family 50

Basic information

Region (hg38): 1:155135344-155138857

Previous symbols: [ "RAG1AP1" ]

Links

ENSG00000169241 ∙ NCBI:55974 ∙ OMIM:613683 ∙ HGNC:30657 ∙ Uniprot:Q9BRV3 ∙ 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 SLC50A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC50A1 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			5	4		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	4	0

Variants in SLC50A1

This is a list of pathogenic ClinVar variants found in the SLC50A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-155135960-G-C		not specified	Likely benign (Jun 18, 2024)
1-155136299-C-G		not specified	Likely benign (Dec 02, 2024)
1-155136328-G-C		not specified	Uncertain significance (Nov 12, 2024)
1-155137561-C-T		not specified	Uncertain significance (Oct 19, 2024)
1-155137585-A-G		not specified	Likely benign (Apr 24, 2024)
1-155137616-G-A		not specified	Uncertain significance (Dec 11, 2023)
1-155137652-G-A		not specified	Uncertain significance (Jan 23, 2023)
1-155138043-T-G		not specified	Uncertain significance (Apr 17, 2023)
1-155138219-T-C		not specified	Likely benign (Aug 12, 2022)
1-155138271-T-C		not specified	Uncertain significance (Jan 03, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC50A1	protein_coding	protein_coding	ENST00000368404	6	3510

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00193	0.915	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.932	97	126	0.767	0.00000647	1408
Missense in Polyphen		30	39.797	0.75383		492
Synonymous	0.393	47	50.6	0.930	0.00000250	457
Loss of Function	1.51	6	11.5	0.520	5.56e-7	121

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates sugar transport across membranes. May stimulate V(D)J recombination by the activation of RAG1. {ECO:0000269|PubMed:21107422}.
• Pathway: SLC-mediated transmembrane transport;Transport of small molecules;Cellular hexose transport (Consensus)

Recessive Scores

• pRec: 0.155

Intolerance Scores

• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.128
• hipred: N
• hipred_score: 0.338
• ghis: 0.584

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc50a1

Gene ontology

• Biological process: hexose transmembrane transport;glucoside transport;positive regulation of gene expression, epigenetic
• Cellular component: Golgi membrane;nucleus;Golgi apparatus;plasma membrane;endomembrane system;integral component of membrane
• Molecular function: glucoside transmembrane transporter activity;sugar transmembrane transporter activity