SLC31A2

protein-coding

solute carrier family 31 member 2, the group of Solute carrier family 31

Gene summary

Enables copper ion transmembrane transporter activity. Involved in copper ion import. Located in late endosome membrane; lysosomal membrane; and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

COPT2

MANE transcript

NM_001860.3

Inheritance

—

ClinVar variants

U:13B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.03

Max pathogenic AF

—

Genomic locus

chr9:113,150,976-113,164,140

External References & Databases

Ensembl (ENSG00000136867)

Transcript & Mutation Effects

hg38 • Region Span ~13.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC31A2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 13

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001860.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			12 clinvar	1 clinvar		13
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	13	1	0	14

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001860.3	RefSeq	NP_001851.1	4	MANE Select
ENST00000259392.8	Ensembl	ENSP00000259392.3	4	MANE Select
ENST00000374220.3	Ensembl	ENSP00000363337.3	4	Standard
ENST00001003680.1	Ensembl	ENSP00000673497.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Copper homeostasis

Biological Process

copper ion transport
cellular copper ion homeostasis
copper ion transmembrane transport
regulation of copper ion transmembrane transport

Molecular Function

copper ion transmembrane transporter activity

Cellular Component

late endosome
plasma membrane
integral component of plasma membrane
recycling endosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000259392
Coding exons: 4
Length: 13196
Individuals with no LoFs: 124796
Homozygous LoFs: 0
Heterozygous LoFs: 27
Defined: 124823
p: 0.000108

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.571	64	78.2	0.818	0.00000383	921
Missense (PolyPhen)		26	30.721	0.84633		414
Synonymous	1.04	25	32.6	0.768	0.00000181	297
Loss of Function	-0.0629	6	5.84	1.03	2.48e-7	70

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00013	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000098	0.000097	rare
South Asian	0.00020	0.00020	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in low-affinity copper uptake. {ECO:0000305}.;

Recessive Scores

pRec: 0.0980

Intolerance Scores

LoFtool: 0.706
RVIS EVS: -0.05
RVIS percentile EVS: 49.39

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.186

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium