SLC38A6

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

Basic information

Region (hg38): 14:60981114-61114316

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.

not_specified (42 variants)
not_provided (1 variants)

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. These statistics are base on transcript: NM_000153811.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			38 clinvar	4 clinvar		42
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	38	5	0

Loading clinvar variants...

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
Phenotype

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