SLC31A1
solute carrier family 31 member 1, the group of Solute carrier family 31
Basic information
Region (hg38): 9:113221544-113264492
Previous symbols: [ "COPT1" ]
Links
Phenotypes
GenCC
Source:
- neurodegeneration and seizures due to copper transport defect (Limited), mode of inheritance: Unknown
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Neurodegeneration and seizures due to copper transport defect | AR | Biochemical | The condition can have neurologic sequelae, and medical management (eg, with copper histidinate) has been reported in having some benefit related to both clinical and biochemical parameters | Biochemical; Neurologic | 35913762; 36562171 |
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 SLC31A1 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 | 1 | |||||
| missense | 12 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 1 | 9 | 1 | 2 |
Variants in SLC31A1
This is a list of pathogenic ClinVar variants found in the SLC31A1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-113256173-A-G | not specified | Uncertain significance (Mar 29, 2022) | ||
| 9-113256204-A-C | not specified | Likely benign (Apr 19, 2024) | ||
| 9-113256221-C-G | Benign (Dec 31, 2019) | |||
| 9-113256224-A-G | not specified | Likely benign (Feb 02, 2024) | ||
| 9-113256254-G-A | not specified | Uncertain significance (Dec 20, 2023) | ||
| 9-113257113-C-G | not specified | Uncertain significance (Sep 27, 2024) | ||
| 9-113257116-A-G | not specified | Uncertain significance (Aug 10, 2021) | ||
| 9-113257144-T-C | not specified | Uncertain significance (Aug 05, 2024) | ||
| 9-113257149-C-A | not specified | Uncertain significance (Feb 14, 2023) | ||
| 9-113257174-A-G | not specified | Uncertain significance (May 25, 2022) | ||
| 9-113258727-T-C | Neurodegeneration and seizures due to copper transport defect | Likely pathogenic (Nov 09, 2022) | ||
| 9-113258766-G-T | not specified | Uncertain significance (Oct 26, 2022) | ||
| 9-113258775-G-A | Neurodegeneration and seizures due to copper transport defect | Pathogenic (Mar 30, 2023) | ||
| 9-113258799-A-G | not specified | Uncertain significance (Jan 10, 2022) | ||
| 9-113258856-C-G | not specified | Uncertain significance (Sep 23, 2023) | ||
| 9-113260405-G-A | not specified | Uncertain significance (Feb 07, 2023) | ||
| 9-113260425-C-T | Benign (Dec 31, 2019) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SLC31A1 | protein_coding | protein_coding | ENST00000374212 | 4 | 44867 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0654 | 0.877 | 125731 | 0 | 6 | 125737 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.08 | 75 | 106 | 0.705 | 0.00000533 | 1271 |
| Missense in Polyphen | 18 | 37.027 | 0.48613 | 466 | ||
| Synonymous | -0.213 | 37 | 35.4 | 1.05 | 0.00000185 | 353 |
| Loss of Function | 1.60 | 3 | 7.84 | 0.383 | 4.21e-7 | 89 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000352 | 0.0000352 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: High-affinity, saturable copper transporter involved in dietary copper uptake. {ECO:0000269|PubMed:11734551}.;
- Pathway
- Mineral absorption - Homo sapiens (human);Platinum Pathway, Pharmacokinetics/Pharmacodynamics;Copper homeostasis;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Metal ion SLC transporters
(Consensus)
Recessive Scores
- pRec
- 0.122
Intolerance Scores
- loftool
- 0.277
- rvis_EVS
- 0.08
- rvis_percentile_EVS
- 59.76
Haploinsufficiency Scores
- pHI
- 0.123
- hipred
- N
- hipred_score
- 0.431
- ghis
- 0.456
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.243
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slc31a1
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; embryo phenotype; pigmentation phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); 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); growth/size/body region phenotype; hematopoietic system 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); cellular phenotype; homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- slc31a1
- Affected structure
- whole organism
- Phenotype tag
- abnormal
- Phenotype quality
- unpigmented
Gene ontology
- Biological process
- copper ion transport;drug transmembrane transport;cellular copper ion homeostasis;cellular response to cisplatin;copper ion import across plasma membrane
- Cellular component
- late endosome;plasma membrane;integral component of plasma membrane;neuronal cell body;recycling endosome
- Molecular function
- copper ion transmembrane transporter activity;identical protein binding