SLC7A4

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

Basic information

Region (hg38): 22:21028718-21032840

Links

ENSG00000099960 ∙ NCBI:6545 ∙ OMIM:603752 ∙ HGNC:11062 ∙ Uniprot:O43246 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC7A4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC7A4 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			71	5	1	77
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	71	7	2

Variants in SLC7A4

This is a list of pathogenic ClinVar variants found in the SLC7A4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
22-21029140-A-T		not specified	Uncertain significance (Jul 31, 2023)
22-21029167-C-T		not specified	Likely benign (Feb 01, 2025)
22-21029179-C-T		not specified	Uncertain significance (Oct 06, 2022)
22-21029213-C-T		not specified	Uncertain significance (Feb 05, 2024)
22-21029221-A-G		not specified	Uncertain significance (Nov 13, 2024)
22-21029230-C-T		not specified	Uncertain significance (Apr 19, 2023)
22-21029359-C-T		not specified	Uncertain significance (Jan 19, 2024)
22-21029368-G-A		not specified	Uncertain significance (Nov 12, 2024)
22-21029727-C-T		not specified	Likely benign (Dec 14, 2022)
22-21029728-G-A		not specified	Uncertain significance (Jun 05, 2024)
22-21029731-A-G		not specified	Uncertain significance (Dec 03, 2021)
22-21029749-C-G		not specified	Uncertain significance (May 21, 2024)
22-21029758-G-A		not specified	Uncertain significance (Dec 20, 2023)
22-21029782-T-TG			Likely benign (Mar 29, 2018)
22-21029863-T-A		not specified	Uncertain significance (Dec 14, 2023)
22-21029865-A-T		not specified	Uncertain significance (Aug 02, 2021)
22-21029866-T-C		not specified	Uncertain significance (May 18, 2023)
22-21029905-C-G		not specified	Uncertain significance (Sep 22, 2023)
22-21029907-G-A		not specified	Uncertain significance (Nov 26, 2024)
22-21029915-G-T		not specified	Uncertain significance (Dec 12, 2023)
22-21029923-C-A		not specified	Uncertain significance (Jan 22, 2025)
22-21029974-C-T		not specified	Uncertain significance (Dec 03, 2024)
22-21029995-T-C		not specified	Likely benign (Nov 07, 2022)
22-21030006-T-C		not specified	Uncertain significance (Aug 02, 2021)
22-21030040-T-A		not specified	Uncertain significance (Jan 21, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC7A4	protein_coding	protein_coding	ENST00000382932	4	4123

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.83e-7	0.526	125375	3	356	125734	0.00143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0725	393	397	0.990	0.0000252	4017
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00910	0.00905
Ashkenazi Jewish	0.000104	0.0000992
East Asian	0.000329	0.000326
Finnish	0.000246	0.000231
European (Non-Finnish)	0.000354	0.000343
Middle Eastern	0.000329	0.000326
South Asian	0.000642	0.000588
Other	0.000524	0.000489

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.408
• hipred: N
• hipred_score: 0.299
• ghis: 0.482

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.279

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc7a4

Gene ontology

• Biological process: cellular amino acid metabolic process;basic amino acid transmembrane transport
• Cellular component: integral component of membrane
• Molecular function: basic amino acid transmembrane transporter activity