CUTC

protein-coding

cutC copper transporter

Gene summary

Members of the CUT family of copper transporters are associated with copper homeostasis and are involved in the uptake, storage, delivery, and efflux of copper (Gupta et al., 1995 [PubMed 7635807]; Li et al., 2005 [PubMed 16182249]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_015960.3

Inheritance

—

ClinVar variants

U:49B:1

Top phenotype

Leigh syndrome

gnomAD constraint

pLI —, LoF o/e 0.47

Max pathogenic AF

—

Genomic locus

chr10:99,702,558-99,756,134

External References & Databases

Ensembl (ENSG00000119929)

Transcript & Mutation Effects

hg38 • Region Span ~53.6 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 CUTC variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 41

Leigh syndromeTotal: 7

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015960.3. 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			5 clinvar			5
missense			42 clinvar	1 clinvar		43
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	49	1	0	50

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015960.3	RefSeq	NP_057044.2	9	MANE Select
ENST00000370476.10	Ensembl	ENSP00000359507.5	9	MANE Select
ENST00000370472.4	Ensembl	ENSP00000359503.4	6	Standard
ENST00000471520.5	Ensembl	ENSP00000433900.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ion channel transport
Transport of small molecules
Ion transport by P-type ATPases

Biological Process

copper ion transport
protein tetramerization
copper ion homeostasis

Molecular Function

copper ion binding
protein binding

Cellular Component

nucleus
nucleoplasm
nucleolus
cytoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370476
Coding exons: 9
Length: 53577
Individuals with no LoFs: 125643
Homozygous LoFs: 1
Heterozygous LoFs: 103
Defined: 125747
p: 0.000414

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.585	136	157	0.869	0.00000840	1732
Missense (PolyPhen)		47	51.29	0.91636		525
Synonymous	0.898	45	53.3	0.844	0.00000255	559
Loss of Function	2.04	8	17.1	0.468	9.63e-7	193

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00043	0.00043	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00065	0.00065	rare
South Asian	0.000099	0.000098	rare
Other	0.0011	0.00098	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in copper homeostasis. Can bind one Cu(1+) per subunit. {ECO:0000269|PubMed:16182249, ECO:0000269|PubMed:19878721}.;

Recessive Scores

pRec: 0.173

Intolerance Scores

LoFtool: 0.597
RVIS EVS: -0.3
RVIS percentile EVS: 32.62

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.923

Gene Damage Prediction

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