SLC31A2

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

Basic information

Region (hg38): 9:113150975-113164140

Previous symbols: [ "COPT2" ]

Links

ENSG00000136867 ∙ NCBI:1318 ∙ OMIM:603088 ∙ HGNC:11017 ∙ Uniprot:O15432 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC31A2 gene.

• Inborn genetic diseases (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC31A2 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						0
missense			5	1		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	1	0

Variants in SLC31A2

This is a list of pathogenic ClinVar variants found in the SLC31A2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-113151078-G-A		not specified	Uncertain significance (Sep 27, 2022)
9-113157729-G-A		not specified	Uncertain significance (Apr 26, 2023)
9-113157757-C-T		not specified	Uncertain significance (Nov 03, 2022)
9-113157772-T-C		not specified	Uncertain significance (Jun 10, 2022)
9-113157790-G-A		not specified	Likely benign (Nov 08, 2022)
9-113161590-A-G		not specified	Uncertain significance (Mar 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC31A2	protein_coding	protein_coding	ENST00000259392	4	13196

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000852	0.340	124796	0	27	124823	0.000108

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.571	64	78.2	0.818	0.00000383	921
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000304	0.000302
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000978	0.0000972
Middle Eastern	0.00	0.00
South Asian	0.000196	0.000196
Other	0.000331	0.000329

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in low-affinity copper uptake. {ECO:0000305}.
• Pathway: Copper homeostasis (Consensus)

Recessive Scores

• pRec: 0.0980

Intolerance Scores

• loftool: 0.706
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.125
• hipred: N
• hipred_score: 0.153
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.186

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc31a2

Gene ontology

• Biological process: copper ion transport;cellular copper ion homeostasis;copper ion transmembrane transport;regulation of copper ion transmembrane transport
• Cellular component: late endosome;plasma membrane;integral component of plasma membrane;recycling endosome
• Molecular function: copper ion transmembrane transporter activity