SLC38A6

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

Basic information

Region (hg38): 14:60981114-61114316

Links

ENSG00000139974NCBI:145389OMIM:616518HGNC:19863Uniprot:Q8IZM9AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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.

EffectPLPVUSLBBSum
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

GeneTypeBio TypeTranscript Coding Exons Length
SLC38A6protein_codingprotein_codingENST00000354886 17102620
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.38e-200.00097612559401541257480.000613
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.4702602401.090.00001083342
Missense in Polyphen8387.0440.953541226
Synonymous-0.6689284.21.090.00000392993
Loss of Function-0.3302927.11.070.00000124377

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001350.00133
Ashkenazi Jewish0.002820.00278
East Asian0.001570.00152
Finnish0.00004620.0000462
European (Non-Finnish)0.0004230.000396
Middle Eastern0.001570.00152
South Asian0.0005670.000523
Other0.001080.000978

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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