NDUFC2-KCTD14

NDUFC2-KCTD14 readthrough

Basic information

Region (hg38): 11:78016971-78079865

Links

ENSG00000259112 ∙ NCBI:100532726 ∙ ∙ HGNC:42956 ∙ Uniprot:E9PQ53 ∙ 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 NDUFC2-KCTD14 gene.

• Inborn genetic diseases (12 variants)
• not provided (3 variants)
• Mitochondrial complex 1 deficiency, nuclear type 36 (2 variants)
• Mitochondrial disease (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NDUFC2-KCTD14 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	1		4			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	1		5	1	1	8
Total	2	0	9	1	1

Variants in NDUFC2-KCTD14

This is a list of pathogenic ClinVar variants found in the NDUFC2-KCTD14 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-78016975-A-C		not specified	Uncertain significance (Mar 30, 2024)
11-78017021-C-T		not specified	Uncertain significance (Aug 12, 2021)
11-78017034-C-A		not specified	Uncertain significance (Jun 16, 2024)
11-78017119-C-T		not specified	Uncertain significance (Apr 13, 2022)
11-78017123-C-T		not specified	Uncertain significance (Jan 08, 2024)
11-78017228-T-C		not specified	Uncertain significance (Sep 14, 2022)
11-78017229-G-T		not specified	Uncertain significance (Mar 06, 2023)
11-78017243-C-T		not specified	Uncertain significance (Dec 08, 2023)
11-78017246-C-A		not specified	Uncertain significance (Apr 17, 2023)
11-78023182-G-T		not specified	Uncertain significance (Aug 09, 2021)
11-78038702-C-T		not specified	Uncertain significance (Jul 12, 2022)
11-78038743-A-G		not specified	Uncertain significance (Jan 31, 2023)
11-78038755-C-A		not specified	Uncertain significance (Aug 30, 2022)
11-78063910-A-G		not specified	Uncertain significance (Apr 07, 2023)
11-78063937-G-A		not specified	Uncertain significance (Apr 15, 2024)
11-78063973-T-C		not specified	Uncertain significance (Jul 14, 2021)
11-78063993-C-T		not specified	Uncertain significance (Dec 20, 2022)
11-78063999-G-A		not specified	Uncertain significance (Jun 02, 2023)
11-78064110-C-T		not specified	Uncertain significance (Dec 16, 2022)
11-78064119-T-A		not specified	Uncertain significance (Mar 30, 2024)
11-78064163-G-C		not specified	Uncertain significance (Feb 27, 2024)
11-78064212-G-A		not specified	Uncertain significance (Mar 25, 2024)
11-78064306-C-T			Benign (Dec 31, 2019)
11-78069876-C-T			Likely benign (Sep 01, 2022)
11-78069900-A-G			Likely benign (Jan 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NDUFC2-KCTD14	protein_coding	protein_coding	ENST00000530054	3	62895

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.657	0.321	117701	0	2	117703	0.00000850

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.386	58	66.9	0.867	0.00000401	707
Missense in Polyphen		29	32.055	0.9047		327
Synonymous	0.654	21	25.2	0.834	0.00000123	229
Loss of Function	1.72	0	3.46	0.00	1.44e-7	50

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000113	0.000113
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000113	0.000113
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone (By similarity). {ECO:0000250}.
• Pathway: Retrograde endocannabinoid signaling - Homo sapiens (human);Non-alcoholic fatty liver disease (NAFLD) - Homo sapiens (human);Alzheimer,s disease - Homo sapiens (human);Huntington,s disease - Homo sapiens (human);Thermogenesis - Homo sapiens (human);Oxidative phosphorylation - Homo sapiens (human);Parkinson,s disease - Homo sapiens (human) (Consensus)

Intolerance Scores

• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.11

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.164

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Biological process: mitochondrial electron transport, NADH to ubiquinone
• Cellular component: mitochondrion;mitochondrial inner membrane;mitochondrial respiratory chain complex I;integral component of membrane;respirasome
• Molecular function: NADH dehydrogenase (ubiquinone) activity