SLC7A3

protein-coding

solute carrier family 7 member 3, the group of Solute carrier family 7

Gene summary

This gene encodes a member of the solute carrier family 7. The encoded protein is a sodium-independent cationic amino acid transporter. Alternate splicing results in multiple transcripts that encoded the same protein.[provided by RefSeq, May 2010]

MANE transcript

NM_032803.6

Inheritance

ClinVar variants

U:50B:13

Top phenotype

SLC7A3-related disorder

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chrX:70,925,579-70,931,125

External References & Databases

Ensembl (ENSG00000165349)

Transcript & Mutation Effects

hg38 • Region Span ~5.5 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

autism spectrum disorderLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0005258

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC7A3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 44

SLC7A3-related disorderTotal: 10

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032803.6. 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			2 clinvar	7 clinvar	1 clinvar	10
missense			48 clinvar	5 clinvar		53
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	50	12	1	63

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 41 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032803.6	RefSeq	NP_116192.4	11	MANE Select
ENST00000374299.8	Ensembl	ENSP00000363417.3	11	MANE Select
NM_001048164.3	RefSeq	NP_001041629.1	11	Standard
ENST00000298085.4	Ensembl	ENSP00000298085.4	11	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
slc7a3a	Danio rerio	Structure: whole organism Quality: decreased size abnormal

Gene / Model

Organism

Observed Phenotype

slc7a3a

Danio rerio

Structure: whole organism

Quality: decreased size

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Biopterin 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

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
amino acid transmembrane transporter activity
arginine transmembrane transporter activity
L-lysine transmembrane transporter activity

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000374299
Coding exons: 11
Length: 5544
Individuals with no LoFs: 125640
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 125641
p: 0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.90	162	246	0.659	0.0000196	3934
Missense (PolyPhen)		17	54.584	0.31145		1117
Synonymous	-0.355	102	97.5	1.05	0.00000778	1341
Loss of Function	3.75	0	16.4	0.00	0.00000111	292

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000012	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Mediates the uptake of the cationic amino acids arginine, lysine and ornithine in a sodium-independent manner. {ECO:0000269|PubMed:11591158}.;

Recessive Scores

pRec: 0.151

Intolerance Scores

LoFtool: 0.0426
RVIS EVS: -0.47
RVIS percentile EVS: 23.43

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0456

Gene Damage Prediction

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