SLC36A1
Basic information
Region (hg38): 5:151437046-151492379
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 1 | |||||
missense | 50 | 55 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 52 | 4 | 2 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SLC36A1 | protein_coding | protein_coding | ENST00000243389 | 10 | 55336 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00000140 | 0.958 | 125672 | 0 | 76 | 125748 | 0.000302 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.38 | 220 | 286 | 0.770 | 0.0000164 | 3099 |
Missense in Polyphen | 49 | 81.966 | 0.59781 | 988 | ||
Synonymous | 0.0328 | 123 | 123 | 0.996 | 0.00000764 | 989 |
Loss of Function | 1.92 | 13 | 22.9 | 0.567 | 0.00000133 | 230 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00154 | 0.00154 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000599 | 0.000598 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000160 | 0.000158 |
Middle Eastern | 0.000599 | 0.000598 |
South Asian | 0.000131 | 0.000131 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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