ATPAF2

ATP synthase mitochondrial F1 complex assembly factor 2, the group of Mitochondrial respiratory chain complex assembly factors

Basic information

Region (hg38): 17:17977408-18039209

Links

ENSG00000171953 ∙ NCBI:91647 ∙ OMIM:608918 ∙ HGNC:18802 ∙ Uniprot:Q8N5M1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• mitochondrial complex V (ATP synthase) deficiency, nuclear type 1 (Limited), mode of inheritance: AR
• mitochondrial proton-transporting ATP synthase complex deficiency (Supportive), mode of inheritance: AR
• mitochondrial complex V (ATP synthase) deficiency, nuclear type 1 (Limited), mode of inheritance: AR
• mitochondrial disease (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Mitochondrial complex V (ATP synthase) deficiency, nuclear type 1	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Biochemical; Cardiovascular; Musculoskeletal; Neurologic	14757859; 20566710

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATPAF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATPAF2 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	24	1	26
missense			56	2	1	59
nonsense			1			1
start loss						0
frameshift		1	2			3
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region			5	4		9
non coding			23	28	14	65
Total	0	1	84	54	16

Variants in ATPAF2

This is a list of pathogenic ClinVar variants found in the ATPAF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-17977619-G-T			Likely benign (Apr 01, 2023)
17-17977662-G-A		not specified	Uncertain significance (Feb 27, 2024)
17-17983828-A-G		not specified	Uncertain significance (Nov 14, 2023)
17-17983830-A-G		not specified	Uncertain significance (Dec 27, 2023)
17-17983872-A-G			Likely benign (Jan 01, 2023)
17-17983912-G-T		not specified	Uncertain significance (Sep 22, 2023)
17-17983935-G-C		not specified	Uncertain significance (Feb 23, 2023)
17-17987958-A-G		not specified	Uncertain significance (Aug 23, 2021)
17-17988013-G-A		not specified	Uncertain significance (Oct 03, 2022)
17-17988045-G-A		not specified	Uncertain significance (Jan 31, 2023)
17-17988070-G-A		not specified	Uncertain significance (Jul 06, 2021)
17-17992834-G-A		not specified	Uncertain significance (Jun 02, 2024)
17-17992894-C-T		not specified	Uncertain significance (Feb 05, 2024)
17-17992895-G-A		not specified	Uncertain significance (Jul 27, 2022)
17-17994359-C-G		not specified	Uncertain significance (Jun 13, 2022)
17-17994368-G-A		not specified	Uncertain significance (Jan 29, 2024)
17-17994379-G-C		not specified	Uncertain significance (Nov 23, 2021)
17-17994390-C-T		not specified	Uncertain significance (Sep 26, 2023)
17-17994395-C-T		not specified	Uncertain significance (Feb 28, 2023)
17-17995027-C-T		not specified	Uncertain significance (Aug 22, 2023)
17-17997542-G-A		not specified	Uncertain significance (Oct 25, 2023)
17-17997564-G-A		not specified	Likely benign (Dec 06, 2022)
17-18004460-T-A		not specified	Uncertain significance (Dec 19, 2022)
17-18006186-A-C		not specified	Uncertain significance (Jun 16, 2024)
17-18006198-T-C		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATPAF2	protein_coding	protein_coding	ENST00000474627	8	61801

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.21e-9	0.143	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.689	142	167	0.850	0.00000964	1868
Missense in Polyphen		21	40.379	0.52007		491
Synonymous	0.603	66	72.5	0.910	0.00000450	578
Loss of Function	0.286	14	15.2	0.921	6.62e-7	172

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000613	0.000608
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000891	0.0000879
Middle Eastern	0.000163	0.000163
South Asian	0.0000670	0.0000653
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the assembly of the F1 component of the mitochondrial ATP synthase (ATPase). {ECO:0000269|PubMed:11410595}.

Recessive Scores

• pRec: 0.146

Intolerance Scores

• loftool: 0.548
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.2

Haploinsufficiency Scores

• pHI: 0.146
• hipred: Y
• hipred_score: 0.673
• ghis: 0.534

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.628

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atpaf2
• Phenotype: skeleton phenotype; growth/size/body region phenotype; craniofacial phenotype

Gene ontology

• Biological process: proton-transporting ATP synthase complex assembly
• Cellular component: mitochondrion;cytosol;nuclear speck
• Molecular function: protein binding