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

Clinical Genomic Database

Source: CGD

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 ClinVar and linked to the SLC31A1 gene.

• not_specified (20 variants)
• not_provided (3 variants)
• Neurodegeneration_and_seizures_due_to_copper_transport_defect (3 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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1		1	2
missense	1	1	18	2	1	23
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	1	1	19	2	2

Highest pathogenic variant AF is 0.0000020521745

GnomAD

Source: gnomAD

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
		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: 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

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

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