SLC38A6

solute carrier family 38 member 6, the group of Solute carrier family 38

Basic information

Region (hg38): 14:60981113-61114316

Links

ENSG00000139974 ∙ NCBI:145389 ∙ OMIM:616518 ∙ HGNC:19863 ∙ Uniprot:Q8IZM9 ∙ 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 SLC38A6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC38A6 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						0
missense			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	0

Variants in SLC38A6

This is a list of pathogenic ClinVar variants found in the SLC38A6 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-60981344-G-A		not specified	Uncertain significance (Aug 19, 2023)
14-60982520-C-G		not specified	Uncertain significance (Feb 28, 2024)
14-60982529-C-T		not specified	Uncertain significance (Jun 13, 2024)
14-60982583-A-C		not specified	Uncertain significance (Aug 08, 2023)
14-60982587-G-A		not specified	Uncertain significance (Apr 24, 2024)
14-60984776-C-T		not specified	Uncertain significance (Dec 28, 2023)
14-61015906-G-A		not specified	Uncertain significance (Oct 26, 2022)
14-61015916-A-G			Uncertain significance (Aug 07, 2018)
14-61019561-A-G		not specified	Uncertain significance (Mar 15, 2024)
14-61030445-C-G		not specified	Uncertain significance (Sep 27, 2021)
14-61030469-T-C		not specified	Uncertain significance (Dec 11, 2023)
14-61030483-C-T		not specified	Uncertain significance (Aug 02, 2021)
14-61037100-G-C		not specified	Uncertain significance (Apr 07, 2023)
14-61037123-G-A		not specified	Uncertain significance (Jan 23, 2023)
14-61037676-C-G		not specified	Uncertain significance (Jul 29, 2023)
14-61043195-G-A		not specified	Likely benign (Jan 29, 2024)
14-61045353-A-G		not specified	Uncertain significance (Jan 19, 2024)
14-61045394-T-C		not specified	Uncertain significance (Dec 14, 2021)
14-61045418-C-T		not specified	Uncertain significance (May 15, 2024)
14-61046104-G-A		not specified	Uncertain significance (Nov 18, 2022)
14-61046125-A-G		not specified	Uncertain significance (Feb 28, 2023)
14-61050569-T-C		not specified	Uncertain significance (Aug 12, 2021)
14-61050574-A-G		not specified	Uncertain significance (Jan 19, 2024)
14-61052070-A-G		not specified	Likely benign (Apr 19, 2024)
14-61052077-C-T		not specified	Uncertain significance (Apr 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC38A6	protein_coding	protein_coding	ENST00000354886	17	102620

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.38e-20	0.000976	125594	0	154	125748	0.000613

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.470	260	240	1.09	0.0000108	3342
Missense in Polyphen		83	87.044	0.95354		1226
Synonymous	-0.668	92	84.2	1.09	0.00000392	993
Loss of Function	-0.330	29	27.1	1.07	0.00000124	377

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00135	0.00133
Ashkenazi Jewish	0.00282	0.00278
East Asian	0.00157	0.00152
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000423	0.000396
Middle Eastern	0.00157	0.00152
South Asian	0.000567	0.000523
Other	0.00108	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable sodium-dependent amino acid/proton antiporter, could be a neuronal transporter for glutamate. {ECO:0000250|UniProtKB:G3UVW3}.

Recessive Scores

• pRec: 0.287

Intolerance Scores

• loftool: 0.988
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

• pHI: 0.0522
• hipred: N
• hipred_score: 0.123
• ghis: 0.548

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0354

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc38a6

Gene ontology

• Biological process: amino acid transmembrane transport;sodium ion transport
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: amino acid transmembrane transporter activity