NDUFAF7

NADH:ubiquinone oxidoreductase complex assembly factor 7, the group of Mitochondrial respiratory chain complex assembly factors|7BS protein arginine methyltranferases

Basic information

Region (hg38): 2:37231630-37253403

Previous symbols: [ "C2orf56" ]

Links

ENSG00000003509 ∙ NCBI:55471 ∙ OMIM:615898 ∙ HGNC:28816 ∙ Uniprot:Q7L592 ∙ 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 NDUFAF7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NDUFAF7 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	14	2	17
missense		1	33	1	3	38
nonsense			1			1
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	5	1	7
non coding			1	23	23	47
Total	0	2	36	38	28

Variants in NDUFAF7

This is a list of pathogenic ClinVar variants found in the NDUFAF7 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-37231668-CA-C		not specified	Benign (Sep 23, 2013)
2-37231669-AG-C			Benign (Aug 31, 2015)
2-37231669-AG-A		not specified	Benign (May 20, 2016)
2-37231670-G-C		not specified	Benign (Nov 19, 2013)
2-37231695-C-T			Likely benign (Apr 19, 2018)
2-37231714-A-G			Benign (Feb 24, 2022)
2-37231724-T-A		not specified	Conflicting classifications of pathogenicity (Nov 21, 2022)
2-37231728-G-A			Benign/Likely benign (Apr 24, 2023)
2-37231755-G-A		not specified	Benign (Jan 26, 2024)
2-37232040-C-T			Benign (Jun 23, 2018)
2-37232065-C-T			Benign (Jun 14, 2018)
2-37232106-C-T			Uncertain significance (Oct 24, 2023)
2-37232117-A-G			Uncertain significance (May 17, 2022)
2-37232127-G-T			Uncertain significance (Jan 02, 2024)
2-37232144-GGGAAT-G			Likely pathogenic (Jan 02, 2018)
2-37232165-C-G		not specified	Benign (Jan 24, 2024)
2-37232184-G-A		not specified	Uncertain significance (Feb 15, 2023)
2-37232189-C-T		not specified	Uncertain significance (May 04, 2023)
2-37232192-A-G		not specified	Uncertain significance (Nov 17, 2022)
2-37232237-A-G			Uncertain significance (Dec 22, 2021)
2-37232245-G-C			Uncertain significance (Jul 06, 2022)
2-37232265-A-C			Uncertain significance (Mar 18, 2022)
2-37232270-T-C		not specified	Likely benign (Apr 07, 2017)
2-37232270-T-G		not specified	Likely benign (Jun 29, 2016)
2-37232527-G-T			Benign (Jun 14, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NDUFAF7	protein_coding	protein_coding	ENST00000002125	10	21773

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.08e-19	0.000641	125657	0	91	125748	0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.05	283	237	1.19	0.0000120	2860
Missense in Polyphen		81	83.096	0.97477		1044
Synonymous	-1.22	100	85.6	1.17	0.00000441	864
Loss of Function	-0.670	27	23.5	1.15	0.00000134	264

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000620	0.000619
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000490	0.000489
Finnish	0.000246	0.000231
European (Non-Finnish)	0.000406	0.000396
Middle Eastern	0.000490	0.000489
South Asian	0.000392	0.000392
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Arginine methyltransferase involved in the assembly or stability of mitochondrial NADH:ubiquinone oxidoreductase complex (complex I) (PubMed:20406883, PubMed:24089531, PubMed:24838397). Acts by mediating symmetric dimethylation of 'Arg-118' of NDUFS2 after it assembles into the complex I, stabilizing the early intermediate complex (PubMed:24089531). {ECO:0000269|PubMed:20406883, ECO:0000269|PubMed:24089531, ECO:0000269|PubMed:24838397}.
• Disease: DISEASE: Note=Defects in NDUFAF7 may be a cause of susceptibility to pathologic myopia, a genetically heterogeneous disorder characterized by extreme, familial, early-onset vision loss and described as myopia accompanied by severe deformation of the eye besides excessive elongation of the eye. {ECO:0000269|PubMed:28837730}.
• Pathway: Thermogenesis - Homo sapiens (human);Respiratory electron transport;The citric acid (TCA) cycle and respiratory electron transport;Metabolism;Complex I biogenesis;Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. (Consensus)

Recessive Scores

• pRec: 0.0919

Intolerance Scores

• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.31

Haploinsufficiency Scores

• pHI: 0.230
• hipred: N
• hipred_score: 0.204
• ghis: 0.527

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ndufaf7
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: ndufaf7
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: peptidyl-arginine methylation, to symmetrical-dimethyl arginine;mitochondrial respiratory chain complex I assembly
• Cellular component: extracellular space;mitochondrion;mitochondrial matrix
• Molecular function: protein binding;methyltransferase activity;enzyme binding;protein-arginine omega-N symmetric methyltransferase activity