NDUFA4L2

NDUFA4 mitochondrial complex associated like 2

Basic information

Region (hg38): 12:57234902-57240715

Links

ENSG00000185633 ∙ NCBI:56901 ∙ ∙ HGNC:29836 ∙ Uniprot:Q9NRX3 ∙ 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 NDUFA4L2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NDUFA4L2 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in NDUFA4L2

This is a list of pathogenic ClinVar variants found in the NDUFA4L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-57235576-C-T		not specified	Uncertain significance (May 17, 2023)
12-57235762-T-C		not specified	Uncertain significance (Dec 05, 2022)
12-57235774-C-A		not specified	Uncertain significance (Oct 05, 2023)
12-57235774-C-T		not specified	Uncertain significance (Feb 16, 2023)
12-57235786-T-G		not specified	Uncertain significance (May 08, 2024)
12-57235798-T-G		not specified	Uncertain significance (Nov 18, 2023)
12-57237052-G-A		not specified	Uncertain significance (Aug 24, 2022)
12-57237052-G-C		not specified	Uncertain significance (Apr 08, 2024)
12-57237060-C-T		not specified	Uncertain significance (May 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NDUFA4L2	protein_coding	protein_coding	ENST00000393825	4	5813

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0864	0.773	125636	0	110	125746	0.000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.510	59	49.0	1.21	0.00000276	552
Missense in Polyphen		16	16.149	0.99078		218
Synonymous	0.875	14	18.8	0.744	0.00000117	154
Loss of Function	1.09	2	4.51	0.444	1.91e-7	56

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000126	0.000124
Ashkenazi Jewish	0.00636	0.00398
East Asian	0.00	0.00
Finnish	0.000105	0.0000924
European (Non-Finnish)	0.000243	0.000211
Middle Eastern	0.00	0.00
South Asian	0.00156	0.00118
Other	0.000993	0.000815

dbNSFP

Source: dbNSFP

• 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);Oxidative phosphorylation (Consensus)

Recessive Scores

• pRec: 0.143

Intolerance Scores

• loftool: 0.736
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

• pHI: 0.493
• hipred: N
• hipred_score: 0.278
• ghis: 0.544

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.824

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ndufa4l2

Gene ontology

• Biological process: electron transport chain;proton transmembrane transport
• Cellular component: mitochondrial respiratory chain complex IV
• Molecular function: cytochrome-c oxidase activity