SLC7A13

protein-coding

solute carrier family 7 member 13, the group of Solute carrier family 7

Gene summary

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

MANE transcript

NM_138817.3

Inheritance

—

ClinVar variants

U:108B:43

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.19

Max pathogenic AF

—

Genomic locus

chr8:86,214,063-86,321,146

External References & Databases

Ensembl (ENSG00000164893)

Transcript & Mutation Effects

hg38 • Region Span ~107.1 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 SLC7A13 variants in ClinVar

2 Conditions Cataloged

not providedTotal: 94

not specifiedTotal: 79

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138817.3. 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				19 clinvar	6 clinvar	25
missense			98 clinvar	13 clinvar	5 clinvar	116
nonsense			5 clinvar			5
start loss			1 clinvar			1
frameshift			4 clinvar			4
splice donor/acceptor (+/-2bp)						0
Total	0	0	108	32	11	151

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_138817.3	RefSeq	NP_620172.2	4	MANE Select
ENST00000297524.8	Ensembl	ENSP00000297524.3	4	MANE Select
ENST00000419776.2	Ensembl	ENSP00000410982.2	5	Standard
ENST00000419776.3	Ensembl	ENSP00000410982.2	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

amino acid transmembrane transport
L-alpha-amino acid transmembrane transport

Molecular Function

L-amino acid transmembrane transporter activity

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000297524
Coding exons: 4
Length: 107095
Individuals with no LoFs: 125706
Homozygous LoFs: 0
Heterozygous LoFs: 29
Defined: 125735
p: 0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.899	282	243	1.16	0.0000117	2985
Missense (PolyPhen)		72	64.237	1.1209		845
Synonymous	-0.705	103	94.3	1.09	0.00000472	994
Loss of Function	-0.688	18	15.1	1.19	7.94e-7	188

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.000089	0.000088	rare
South Asian	0.00016	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Mediates the transport L-aspartate and L-glutamate in a sodium-independent manner. {ECO:0000250}.;

Recessive Scores

pRec: 0.144

Intolerance Scores

LoFtool: 0.240
RVIS EVS: 1.93
RVIS percentile EVS: 97.48

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.106

Gene Damage Prediction

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