ATPAF1

ATP synthase mitochondrial F1 complex assembly factor 1, the group of Mitochondrial respiratory chain complex assembly factors

Basic information

Region (hg38): 1:46632737-46673867

Links

ENSG00000123472 ∙ NCBI:64756 ∙ OMIM:608917 ∙ HGNC:18803 ∙ Uniprot:Q5TC12 ∙ 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 ATPAF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATPAF1 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	1	0

Variants in ATPAF1

This is a list of pathogenic ClinVar variants found in the ATPAF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-46635884-G-C			Likely benign (Jun 01, 2024)
1-46635916-C-T		not specified	Uncertain significance (Jan 10, 2023)
1-46645231-T-A		not specified	Uncertain significance (Dec 21, 2023)
1-46668088-G-A		not specified	Uncertain significance (May 02, 2024)
1-46668157-G-A		not specified	Uncertain significance (Aug 11, 2022)
1-46668230-G-T		not specified	Uncertain significance (Dec 15, 2022)
1-46668231-C-T		not specified	Uncertain significance (Dec 15, 2022)
1-46668259-G-A		not specified	Uncertain significance (May 23, 2023)
1-46668330-C-G		not specified	Uncertain significance (Jun 23, 2023)
1-46668376-C-A		not specified	Uncertain significance (Sep 06, 2022)
1-46671952-G-C		not specified	Uncertain significance (Feb 13, 2024)
1-46671965-C-T		not specified	Uncertain significance (May 16, 2024)
1-46672874-G-C		not specified	Uncertain significance (Aug 30, 2022)
1-46672945-A-G		not specified	Uncertain significance (Oct 27, 2022)
1-46672947-T-C		not specified	Uncertain significance (Dec 06, 2022)
1-46672989-G-A		not specified	Uncertain significance (Nov 09, 2021)
1-46673002-G-C		not specified	Uncertain significance (Dec 19, 2023)
1-46673022-A-T		not specified	Uncertain significance (Sep 25, 2023)
1-46673052-C-T		not specified	Uncertain significance (Oct 12, 2022)
1-46673056-G-A		not specified	Likely benign (Feb 28, 2023)
1-46673110-C-T		not specified	Uncertain significance (Dec 01, 2022)
1-46673121-G-T		not specified	Uncertain significance (Dec 02, 2022)
1-46673160-G-A		not specified	Uncertain significance (Sep 17, 2021)
1-46673194-C-T		not specified	Uncertain significance (Jan 26, 2022)
1-46673292-G-A		not specified	Uncertain significance (Jun 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATPAF1	protein_coding	protein_coding	ENST00000576409	9	41131

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0135	0.980	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.18	108	149	0.727	0.00000791	2233
Missense in Polyphen		33	48.505	0.68034		684
Synonymous	0.0215	52	52.2	0.996	0.00000292	682
Loss of Function	2.40	6	16.5	0.363	7.54e-7	216

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000547	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000714	0.0000703
Middle Eastern	0.0000547	0.0000544
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play an essential role for the assembly of the mitochondrial F1-F0 complex. {ECO:0000250}.

Recessive Scores

• pRec: 0.0994

Intolerance Scores

• rvis_EVS: -0.45
• rvis_percentile_EVS: 24

Haploinsufficiency Scores

• pHI: 0.205
• hipred: Y
• hipred_score: 0.816
• ghis: 0.624

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.683

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atpaf1

Gene ontology

• Biological process: mitochondrial proton-transporting ATP synthase complex assembly
• Cellular component: mitochondrion
• Molecular function: protein binding