SLC1A5

solute carrier family 1 member 5, the group of Solute carrier family 1|Minor histocompatibility antigens

Basic information

Region (hg38): 19:46774883-46788594

Previous symbols: [ "RDRC", "M7V1" ]

Links

ENSG00000105281 ∙ NCBI:6510 ∙ OMIM:109190 ∙ HGNC:10943 ∙ Uniprot:Q15758 ∙ 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 SLC1A5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC1A5 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			36	1	1	38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	36	1	1

Variants in SLC1A5

This is a list of pathogenic ClinVar variants found in the SLC1A5 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-46775514-A-G		not specified	Uncertain significance (Jan 05, 2022)
19-46775535-G-A		not specified	Uncertain significance (Mar 17, 2023)
19-46775563-G-A		not specified	Uncertain significance (Mar 31, 2024)
19-46775658-C-A		not specified	Uncertain significance (Aug 11, 2022)
19-46775673-C-T		not specified	Uncertain significance (Oct 01, 2024)
19-46775731-C-T		not specified	Likely benign (Jul 14, 2021)
19-46775732-G-A		SLC1A5-related disorder	Benign (Feb 14, 2020)
19-46775742-C-T		not specified	Uncertain significance (Jun 10, 2024)
19-46777006-T-G			Benign (May 29, 2018)
19-46777119-A-G		SLC1A5-related disorder	Benign (Jun 26, 2019)
19-46777215-T-C		not specified	Uncertain significance (Mar 20, 2023)
19-46777278-C-T		not specified	Uncertain significance (Aug 12, 2024)
19-46777293-C-T		not specified	Uncertain significance (Jun 05, 2024)
19-46777294-G-A		SLC1A5-related disorder	Benign (Jun 26, 2019)
19-46777299-C-G		not specified	Uncertain significance (Nov 21, 2024)
19-46777307-T-C		not specified	Uncertain significance (Oct 01, 2024)
19-46777332-T-C		not specified	Uncertain significance (Jun 10, 2022)
19-46777337-C-T		not specified	Uncertain significance (May 21, 2024)
19-46777366-C-A		not specified	Uncertain significance (Aug 28, 2024)
19-46778745-G-A		not specified	Uncertain significance (Jun 21, 2021)
19-46778831-C-T		not specified	Uncertain significance (Aug 02, 2021)
19-46778880-C-A		not specified	Uncertain significance (Apr 11, 2023)
19-46778904-C-T		Hereditary spastic paraplegia • not specified	Uncertain significance (Mar 24, 2023)
19-46782437-C-T		not specified	Uncertain significance (Aug 08, 2023)
19-46782438-G-A		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC1A5	protein_coding	protein_coding	ENST00000542575	8	13712

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.169	0.829	125716	0	22	125738	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.86	242	338	0.716	0.0000200	3384
Missense in Polyphen		100	144.59	0.69161		1532
Synonymous	0.640	147	157	0.935	0.0000101	1238
Loss of Function	2.62	4	14.9	0.268	6.41e-7	170

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000156	0.000154
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.0000472	0.0000462
European (Non-Finnish)	0.000108	0.000106
Middle Eastern	0.0000545	0.0000544
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sodium-dependent amino acids transporter that has a broad substrate specificity, with a preference for zwitterionic amino acids. It accepts as substrates all neutral amino acids, including glutamine, asparagine, and branched-chain and aromatic amino acids, and excludes methylated, anionic, and cationic amino acids (PubMed:8702519, PubMed:29872227). Through binding of the fusogenic protein syncytin-1/ERVW-1 may mediate trophoblasts syncytialization, the spontaneous fusion of their plasma membranes, an essential process in placental development (PubMed:10708449, PubMed:23492904). {ECO:0000269|PubMed:10708449, ECO:0000269|PubMed:23492904, ECO:0000269|PubMed:29872227, ECO:0000269|PubMed:8702519}.; FUNCTION: (Microbial infection) Acts as a cell surface receptor for Baboon M7 endogenous virus. {ECO:0000269|PubMed:10196349}.
• Pathway: Central carbon metabolism in cancer - Homo sapiens (human);Protein digestion and absorption - Homo sapiens (human);Warburg Effect;Argininemia;Citrullinemia Type I;Carbamoyl Phosphate Synthetase Deficiency;Argininosuccinic Aciduria;Urea Cycle;Glutaminolysis and Cancer;Ornithine Transcarbamylase Deficiency (OTC Deficiency);mRNA, protein, and metabolite inducation pathway by cyclosporin A;TYROBP Causal Network;Tyrosine metabolism;Amino acid transport across the plasma membrane;Amino acid and oligopeptide SLC transporters;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Histidine metabolism;Methionine and cysteine metabolism;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Aminosugars metabolism;Glycerophospholipid metabolism;Porphyrin metabolism;Glycine, serine, alanine and threonine metabolism (Consensus)

Recessive Scores

• pRec: 0.236

Haploinsufficiency Scores

• pHI: 0.346
• hipred: N
• hipred_score: 0.353
• ghis: 0.414

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.921

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc1a5
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: amino acid transport;glutamine transport;glutamine secretion;neutral amino acid transport;L-serine transport;viral entry into host cell;protein homotrimerization;L-glutamine import across plasma membrane
• Cellular component: plasma membrane;integral component of plasma membrane;membrane;integral component of membrane;melanosome;extracellular exosome
• Molecular function: virus receptor activity;protein binding;amino acid transmembrane transporter activity;neutral amino acid transmembrane transporter activity;L-glutamine transmembrane transporter activity;L-serine transmembrane transporter activity;symporter activity;signaling receptor activity;metal ion binding