SLC1A5

protein-coding

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

Gene summary

The SLC1A5 gene encodes a sodium-dependent neutral amino acid transporter that can act as a receptor for RD114/type D retrovirus (Larriba et al., 2001 [PubMed 11781704]).[supplied by OMIM, Jan 2011]

Previous symbols:

RDRC
M7V1

MANE transcript

NM_005628.3

Inheritance

—

ClinVar variants

U:71B:12

Top phenotype

SLC1A5-related disorder

gnomAD constraint

pLI —, LoF o/e 0.27

Max pathogenic AF

—

Genomic locus

chr19:46,774,883-46,788,594

External References & Databases

Ensembl (ENSG00000105281)

Transcript & Mutation Effects

hg38 • Region Span ~13.7 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC1A5 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 64

SLC1A5-related disorderTotal: 11

not providedTotal: 1

Hereditary spastic paraplegiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005628.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar	2 clinvar	5
missense			66 clinvar	5 clinvar	2 clinvar	73
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	71	8	4	83

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005628.3	RefSeq	NP_005619.1	8	MANE Select
ENST00000542575.6	Ensembl	ENSP00000444408.1	8	MANE Select
NM_001145144.2	RefSeq	NP_001138616.1	5	Standard
NM_001145145.2	RefSeq	NP_001138617.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Central carbon metabolism in cancer - Homo sapiens (human)
Protein digestion and absorption - Homo sapiens (human)
Warburg Effect
Argininemia
Citrullinemia Type I

Biological Process

amino acid transport
glutamine transport
glutamine secretion
neutral amino acid transport
L-serine transport

Molecular Function

virus receptor activity
protein binding
amino acid transmembrane transporter activity
neutral amino acid transmembrane transporter activity
L-glutamine transmembrane transporter activity

Cellular Component

plasma membrane
integral component of plasma membrane
membrane
integral component of membrane
melanosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000542575
Coding exons: 8
Length: 13712
Individuals with no LoFs: 125716
Homozygous LoFs: 0
Heterozygous LoFs: 22
Defined: 125738
p: 0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.86	242	338	0.716	0.0000200	3384
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000063	0.000062	rare
Latino/Admixed American	0.000093	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.236

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.921

Gene Damage Prediction

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