CUTC

cutC copper transporter

Basic information

Region (hg38): 10:99702557-99756134

Links

ENSG00000119929 ∙ NCBI:51076 ∙ OMIM:610101 ∙ HGNC:24271 ∙ Uniprot:Q9NTM9 ∙ 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 CUTC gene.

• Leigh syndrome (12 variants)
• Inborn genetic diseases (11 variants)
• not provided (4 variants)
• Cytochrome-c oxidase deficiency disease (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CUTC 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			1			1
missense			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			9	2	2	13
Total	0	0	22	2	2

Variants in CUTC

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

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

Position	Type	Phenotype	Significance	ClinVar
10-99702592-G-A		not specified	Likely benign (Mar 07, 2023)
10-99702598-C-A		not specified	Uncertain significance (Feb 28, 2023)
10-99702606-G-A		not specified	Uncertain significance (May 18, 2023)
10-99702631-C-T		not specified	Uncertain significance (Jun 07, 2023)
10-99702658-G-A		not specified	Uncertain significance (Aug 30, 2021)
10-99704483-C-T		not specified	Uncertain significance (Oct 25, 2022)
10-99704498-C-T		not specified	Uncertain significance (Nov 22, 2022)
10-99704499-G-A		not specified	Uncertain significance (Jul 12, 2023)
10-99704568-T-C		not specified	Uncertain significance (Sep 14, 2023)
10-99708941-A-G		Leigh syndrome	Likely benign (Jan 12, 2018)
10-99708973-C-G		Leigh syndrome	Uncertain significance (Jan 12, 2018)
10-99708975-C-T		Mitochondrial complex IV deficiency, nuclear type 1	Uncertain significance (Jun 14, 2016)
10-99708979-T-C		Leigh syndrome	Uncertain significance (Jan 12, 2018)
10-99709022-C-T		Leigh syndrome	Uncertain significance (Jan 13, 2018)
10-99709196-G-A		Leigh syndrome	Likely benign (Jan 12, 2018)
10-99709202-C-T		Leigh syndrome	Uncertain significance (Mar 16, 2018)
10-99709233-G-T		Leigh syndrome	Uncertain significance (Jan 12, 2018)
10-99709262-G-A		Leigh syndrome	Uncertain significance (Jan 12, 2018)
10-99709304-A-C		Leigh syndrome	Uncertain significance (Jan 12, 2018)
10-99709472-T-C		Leigh syndrome	Conflicting classifications of pathogenicity (May 01, 2023)
10-99709597-T-C		Leigh syndrome	Uncertain significance (Jan 13, 2018)
10-99709614-G-T		Leigh syndrome	Uncertain significance (Jan 13, 2018)
10-99709659-C-T		Leigh syndrome	Uncertain significance (Jan 13, 2018)
10-99709685-G-C		Leigh syndrome	Uncertain significance (Jan 13, 2018)
10-99709753-A-G		Leigh syndrome	Likely benign (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CUTC	protein_coding	protein_coding	ENST00000370476	9	53577

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000611	0.978	125643	1	103	125747	0.000414

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.585	136	157	0.869	0.00000840	1732
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000742	0.000742
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000652	0.000651
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000993	0.0000980
Other	0.00114	0.000978

dbNSFP

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}.
• Pathway: Ion channel transport;Transport of small molecules;Ion transport by P-type ATPases (Consensus)

Recessive Scores

• pRec: 0.173

Intolerance Scores

• loftool: 0.597
• rvis_EVS: -0.3
• rvis_percentile_EVS: 32.62

Haploinsufficiency Scores

• pHI: 0.136
• hipred: N
• hipred_score: 0.445
• ghis: 0.603

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.923

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cutc

Gene ontology

• Biological process: copper ion transport;protein tetramerization;copper ion homeostasis
• Cellular component: nucleus;nucleoplasm;nucleolus;cytoplasm;cytosol
• Molecular function: copper ion binding;protein binding