SLC36A1

solute carrier family 36 member 1, the group of Solute carrier family 36

Basic information

Region (hg38): 5:151437046-151492379

Links

ENSG00000123643NCBI:206358OMIM:606561HGNC:18761Uniprot:Q7Z2H8AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC36A1 gene.

  • not_specified (54 variants)
  • not_provided (4 variants)
  • Autism (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC36A1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000078483.4. 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
50
clinvar
4
clinvar
1
clinvar
55
nonsense
1
clinvar
1
start loss
0
frameshift
1
clinvar
1
splice donor/acceptor (+/-2bp)
0
Total 0 0 52 4 2
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SLC36A1protein_codingprotein_codingENST00000243389 1055336
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.000001400.9581256720761257480.000302
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.382202860.7700.00001643099
Missense in Polyphen4981.9660.59781988
Synonymous0.03281231230.9960.00000764989
Loss of Function1.921322.90.5670.00000133230

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001540.00154
Ashkenazi Jewish0.000.00
East Asian0.0005990.000598
Finnish0.000.00
European (Non-Finnish)0.0001600.000158
Middle Eastern0.0005990.000598
South Asian0.0001310.000131
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Neutral amino acid/proton symporter. Has a pH-dependent electrogenic transport activity for small amino acids such as glycine, alanine and proline. Besides small apolar L-amino acids, it also recognizes their D-enantiomers and selected amino acid derivatives such as gamma-aminobutyric acid (By similarity). {ECO:0000250, ECO:0000269|PubMed:12809675}.;
Pathway
Protein digestion and absorption - Homo sapiens (human);Amino acid transport across the plasma membrane;Amino acid and oligopeptide SLC transporters;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Proton-coupled neutral amino acid transporters;Histidine metabolism;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Bile acid biosynthesis;Porphyrin metabolism;Glycine, serine, alanine and threonine metabolism (Consensus)

Recessive Scores

pRec
0.149

Intolerance Scores

loftool
0.656
rvis_EVS
-0.62
rvis_percentile_EVS
17.36

Haploinsufficiency Scores

pHI
0.139
hipred
N
hipred_score
0.359
ghis
0.547

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.858

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Slc36a1
Phenotype

Gene ontology

Biological process
amino acid transmembrane transport;ion transport;amino acid transport;L-alanine transport;glycine transport;proline transmembrane transport;proton transmembrane transport
Cellular component
lysosomal membrane;endoplasmic reticulum;plasma membrane;integral component of membrane
Molecular function
amino acid:proton symporter activity;proton transmembrane transporter activity;amino acid transmembrane transporter activity;L-alanine transmembrane transporter activity;glycine transmembrane transporter activity;L-proline transmembrane transporter activity