GeneBe

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

ENSG00000136868 ∙ NCBI:1317 ∙ OMIM:603085 ∙ HGNC:11016 ∙ Uniprot:O15431 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • neurodegeneration and seizures due to copper transport defect (Limited), mode of inheritance: Unknown
  • neurodegeneration and seizures due to copper transport defect (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Neurodegeneration and seizures due to copper transport defectARBiochemicalThe 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 parametersBiochemical; Neurologic35913762; 36562171

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC31A1 gene.

  • not_specified (18 variants)
  • not_provided (3 variants)
  • Neurodegeneration_and_seizures_due_to_copper_transport_defect (2 variants)

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. These statistics are base on transcript: NM_000001859.4. 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
1
clinvar
1
clinvar
16
clinvar
2
clinvar
1
clinvar
 21
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 1 1 16 2 2

Highest pathogenic variant AF is 0.0000020521745

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SLC31A1protein_codingprotein_codingENST00000374212 444867
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.06540.877125731061257370.0000239
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.08751060.7050.000005331271
Missense in Polyphen1837.0270.48613466
Synonymous-0.2133735.41.050.00000185353
Loss of Function1.6037.840.3834.21e-789

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.00003520.0000352
Middle Eastern0.00005440.0000544
South Asian0.000.00
Other0.0001630.000163

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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