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.

not_specified (58 variants)
SLC1A5-related_disorder (9 variants)
not_provided (1 variants)
Hereditary_spastic_paraplegia (1 variants)

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. These statistics are base on transcript: NM_000005628.3. 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				3 clinvar	2 clinvar	5
missense			55 clinvar	4 clinvar	2 clinvar	61
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	55	7	4

Loading clinvar variants...

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