SLC7A1

protein-coding

solute carrier family 7 member 1, the group of Solute carrier family 7

Gene summary

Enables L-arginine transmembrane transporter activity; L-histidine transmembrane transporter activity; and L-lysine transmembrane transporter activity. Involved in carboxylic acid transport. Located in apical plasma membrane and basolateral plasma membrane. Part of protein-containing complex. Is active in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

ERR
ATRC1

MANE transcript

NM_003045.5

Inheritance

—

ClinVar variants

U:55B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.08

Max pathogenic AF

—

Genomic locus

chr13:29,509,414-29,595,688

External References & Databases

Ensembl (ENSG00000139514)

Transcript & Mutation Effects

hg38 • Region Span ~86.3 kb

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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 SLC7A1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 57

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003045.5. 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			1 clinvar	2 clinvar	5 clinvar	8
missense			54 clinvar	3 clinvar	1 clinvar	58
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	55	5	6	66

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_003045.5	RefSeq	NP_003036.1	11	MANE Select
ENST00000380752.10	Ensembl	ENSP00000370128.5	11	MANE Select
ENST00000450494.1	Ensembl	ENSP00000390092.1	1	Standard
ENST00000907882.1	Ensembl	ENSP00000577941.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

MicroRNAs in cancer - Homo sapiens (human)
Biopterin metabolism
Amino acid transport across the plasma membrane
Amino acid and oligopeptide SLC transporters
Transport of inorganic cations/anions and amino acids/oligopeptides

Biological Process

amino acid transport
L-arginine import across plasma membrane
L-ornithine transmembrane transport
L-lysine transmembrane transport

Molecular Function

L-ornithine transmembrane transporter activity
protein binding
amino acid transmembrane transporter activity
arginine transmembrane transporter activity
L-lysine transmembrane transporter activity

Cellular Component

plasma membrane
integral component of plasma membrane
membrane
protein-containing complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000380752
Coding exons: 11
Length: 86279
Individuals with no LoFs: 125744
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125748
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.30	206	389	0.530	0.0000243	4055
Missense (PolyPhen)		67	193.82	0.34568		1957
Synonymous	0.190	167	170	0.981	0.0000124	1326
Loss of Function	4.12	2	23.6	0.0848	0.00000101	297

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: High-affinity, low capacity permease involved in the transport of the cationic amino acids (arginine, lysine and ornithine) in non-hepatic tissues. {ECO:0000269|PubMed:10485994}.;

Recessive Scores

pRec: 0.305

Intolerance Scores

LoFtool: 0.0567
RVIS EVS: -1.22
RVIS percentile EVS: 5.6

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.602

Gene Damage Prediction

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