SLC38A7

solute carrier family 38 member 7, the group of Solute carrier family 38

Basic information

Region (hg38): 16:58665109-58684770

Links

ENSG00000103042 ∙ NCBI:55238 ∙ OMIM:614236 ∙ HGNC:25582 ∙ Uniprot:Q9NVC3 ∙ 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 SLC38A7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC38A7 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
missense			23		2	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	3

Variants in SLC38A7

This is a list of pathogenic ClinVar variants found in the SLC38A7 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-58667396-G-A		not specified	Uncertain significance (Jul 05, 2023)
16-58667410-G-A		not specified	Uncertain significance (Dec 13, 2024)
16-58667412-G-A			Benign (Aug 25, 2017)
16-58671056-A-G		not specified	Uncertain significance (Jul 26, 2022)
16-58671069-C-A		not specified	Uncertain significance (Nov 13, 2023)
16-58671069-C-T		not specified	Uncertain significance (Nov 18, 2022)
16-58671096-C-A		not specified	Uncertain significance (Oct 16, 2023)
16-58671102-C-T		not specified	Uncertain significance (Oct 14, 2021)
16-58671211-C-G		not specified	Uncertain significance (Jan 07, 2025)
16-58671218-C-T		not specified	Uncertain significance (Mar 06, 2023)
16-58672160-C-T		not specified	Uncertain significance (Mar 01, 2023)
16-58672166-C-T		not specified	Uncertain significance (Jul 12, 2022)
16-58672171-A-G		not specified	Uncertain significance (Jun 02, 2023)
16-58672180-G-A		not specified	Uncertain significance (Feb 14, 2025)
16-58672199-C-T		not specified	Uncertain significance (May 14, 2024)
16-58675958-C-T		not specified	Uncertain significance (Nov 22, 2022)
16-58675959-G-A			Benign (Aug 25, 2017)
16-58675976-C-T		not specified	Uncertain significance (Jul 25, 2023)
16-58676315-T-C		not specified	Uncertain significance (Dec 02, 2024)
16-58678414-T-C		not specified	Uncertain significance (Aug 26, 2022)
16-58678445-C-G		not specified	Uncertain significance (May 17, 2023)
16-58678753-A-G		not specified	Uncertain significance (Apr 12, 2024)
16-58678798-A-G		not specified	Uncertain significance (Jan 31, 2023)
16-58678848-C-T		not specified	Uncertain significance (Nov 28, 2023)
16-58678855-C-A		not specified	Uncertain significance (Jan 26, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC38A7	protein_coding	protein_coding	ENST00000570101	10	19996

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000290	0.986	125733	0	14	125747	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.00	228	275	0.830	0.0000164	2961
Missense in Polyphen		86	115.02	0.74769		1243
Synonymous	0.399	113	119	0.953	0.00000803	964
Loss of Function	2.20	11	22.2	0.497	0.00000111	229

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.000113	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000711	0.0000703
Middle Eastern	0.000113	0.000109
South Asian	0.0000706	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates sodium-dependent transport of amino acids, preferentially L-glutamine. {ECO:0000250}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.504
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.51

Haploinsufficiency Scores

• pHI: 0.123
• hipred: N
• hipred_score: 0.488
• ghis: 0.535

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.740

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc38a7

Gene ontology

• Biological process: amino acid transmembrane transport;sodium ion transport;asparagine transport;glutamine transport;branched-chain amino acid transport;L-alanine transport;L-glutamate transmembrane transport;methionine transport;L-serine transport;L-aspartate transmembrane transport;L-histidine transmembrane transport
• Cellular component: integral component of membrane;axon;neuronal cell body
• Molecular function: L-histidine transmembrane transporter activity;L-glutamate transmembrane transporter activity;protein binding;amino acid transmembrane transporter activity;L-amino acid transmembrane transporter activity;L-alanine transmembrane transporter activity;L-asparagine transmembrane transporter activity;L-aspartate transmembrane transporter activity;L-glutamine transmembrane transporter activity;L-leucine transmembrane transporter activity;L-methionine transmembrane transporter activity;L-serine transmembrane transporter activity