SLC38A10
Basic information
Region (hg38): 17:81244811-81295547
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC38A10 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 | 2 | |||||
missense | 55 | 11 | 66 | |||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 55 | 12 | 1 |
Variants in SLC38A10
This is a list of pathogenic ClinVar variants found in the SLC38A10 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
17-81245603-G-A | not specified | Uncertain significance (Aug 10, 2021) | ||
17-81245636-G-A | not specified | Uncertain significance (Oct 26, 2021) | ||
17-81245851-A-G | SLC38A10-related disorder | Likely benign (Apr 28, 2022) | ||
17-81245997-C-G | not specified | Uncertain significance (Jul 13, 2021) | ||
17-81246100-G-A | not specified | Likely benign (Jul 13, 2021) | ||
17-81246137-T-C | SLC38A10-related disorder | Likely benign (May 22, 2020) | ||
17-81246203-T-C | not specified | Likely benign (Jul 26, 2021) | ||
17-81246221-C-A | SLC38A10-related disorder | Uncertain significance (Sep 11, 2024) | ||
17-81246298-C-T | not specified | Likely benign (Sep 01, 2021) | ||
17-81246326-C-T | not specified | Uncertain significance (Sep 01, 2021) | ||
17-81251240-C-T | SLC38A10-related disorder | Likely benign (Aug 12, 2022) | ||
17-81251439-G-A | SLC38A10-related disorder | Likely benign (May 30, 2023) | ||
17-81251510-G-A | not specified | Uncertain significance (May 15, 2023) | ||
17-81251525-G-A | not specified | Likely benign (Dec 14, 2023) | ||
17-81251528-C-T | not specified | Uncertain significance (Dec 03, 2021) | ||
17-81251548-G-A | SLC38A10-related disorder | Likely benign (Sep 25, 2020) | ||
17-81251564-A-C | not specified | Uncertain significance (Jan 04, 2022) | ||
17-81251573-C-A | not specified | Uncertain significance (Jul 14, 2023) | ||
17-81252216-G-T | not specified | Uncertain significance (Nov 07, 2024) | ||
17-81252242-C-A | not specified | Uncertain significance (Aug 02, 2021) | ||
17-81252248-G-A | not specified | Likely benign (Apr 25, 2022) | ||
17-81252251-G-A | not specified | Uncertain significance (Feb 28, 2023) | ||
17-81252258-C-T | not specified | Uncertain significance (Feb 10, 2022) | ||
17-81252291-C-T | not specified | Uncertain significance (Jan 29, 2024) | ||
17-81252330-G-A | not specified | Uncertain significance (Feb 16, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SLC38A10 | protein_coding | protein_coding | ENST00000374759 | 16 | 50548 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
2.43e-10 | 0.970 | 125647 | 0 | 100 | 125747 | 0.000398 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.566 | 679 | 722 | 0.941 | 0.0000475 | 7176 |
Missense in Polyphen | 195 | 232.86 | 0.83741 | 2380 | ||
Synonymous | -0.373 | 331 | 322 | 1.03 | 0.0000238 | 2381 |
Loss of Function | 2.20 | 21 | 35.0 | 0.599 | 0.00000175 | 385 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000465 | 0.000420 |
Ashkenazi Jewish | 0.00124 | 0.00119 |
East Asian | 0.000505 | 0.000489 |
Finnish | 0.000147 | 0.000139 |
European (Non-Finnish) | 0.000472 | 0.000448 |
Middle Eastern | 0.000505 | 0.000489 |
South Asian | 0.000462 | 0.000425 |
Other | 0.000349 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Putative sodium-dependent amino acid/proton antiporter. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.0945
Intolerance Scores
- loftool
- 0.802
- rvis_EVS
- 1.13
- rvis_percentile_EVS
- 92.24
Haploinsufficiency Scores
- pHI
- 0.114
- hipred
- N
- hipred_score
- 0.306
- ghis
- 0.559
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.487
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | High | High | High |
Primary Immunodeficiency | High | High | High |
Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Slc38a10
- Phenotype
- immune system phenotype; skeleton phenotype; vision/eye phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; craniofacial phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan);
Gene ontology
- Biological process
- amino acid transmembrane transport;sodium ion transport;bone development
- Cellular component
- Golgi apparatus;integral component of membrane
- Molecular function
- amino acid transmembrane transporter activity