SLC7A4

protein-coding

solute carrier family 7 member 4, the group of Solute carrier family 7

Gene summary

Predicted to enable amino acid transmembrane transporter activity. Predicted to be involved in amino acid transport. Predicted to be located in membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_004173.3

Inheritance

—

ClinVar variants

U:121B:13

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.76

Max pathogenic AF

—

Genomic locus

chr22:21,028,718-21,032,840

External References & Databases

Ensembl (ENSG00000099960)

Transcript & Mutation Effects

hg38 • Region Span ~4.1 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 SLC7A4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 128

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004173.3. 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				1 clinvar	1 clinvar	2
missense			121 clinvar	9 clinvar	1 clinvar	131
nonsense						0
start loss						0
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)						0
Total	0	0	121	11	2	134

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004173.3	RefSeq	NP_004164.2	4	MANE Select
ENST00000382932.3	Ensembl	ENSP00000372390.2	4	MANE Select
ENST00000403586.5	Ensembl	ENSP00000384278.1	4	Standard
ENST00000403586.6	Ensembl	ENSP00000384278.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cellular amino acid metabolic process
basic amino acid transmembrane transport

Molecular Function

basic amino acid transmembrane transporter activity

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000382932
Coding exons: 4
Length: 4123
Individuals with no LoFs: 125375
Homozygous LoFs: 3
Heterozygous LoFs: 356
Defined: 125734
p: 0.00143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0725	393	397	0.990	0.0000252	4017
Missense (PolyPhen)		89	106.58	0.83503		1282
Synonymous	0.0471	184	185	0.996	0.0000126	1462
Loss of Function	0.900	12	15.9	0.756	6.82e-7	162

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0013	0.0013	notable
Latino/Admixed American	0.0078	0.0077	notable
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00033	0.00033	rare
Finnish	0.00025	0.00023	rare
European (Non-Finnish)	0.00035	0.00034	rare
South Asian	0.00064	0.00059	rare
Other	0.00052	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in the transport of the cationic amino acids (arginine, lysine and ornithine).;

Recessive Scores

pRec: 0.141

Intolerance Scores

LoFtool: 0.0926
RVIS EVS: 0.41
RVIS percentile EVS: 76.51

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.279

Gene Damage Prediction

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