ATPAF1

protein-coding

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

Gene summary

This gene encodes an assembly factor for the F(1) component of the mitochondrial ATP synthase. This protein binds specifically to the F1 beta subunit and is thought to prevent this subunit from forming nonproductive homooligomers during enzyme assembly. Alternatively spliced transcript variants have been identified. [provided by RefSeq, Aug 2011]

MANE transcript

NM_001394565.1

Inheritance

—

ClinVar variants

U:14B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.36

Max pathogenic AF

—

Genomic locus

chr1:46,632,737-46,673,867

External References & Databases

Ensembl (ENSG00000123472)

Transcript & Mutation Effects

hg38 • Region Span ~41.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ATPAF1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 12

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001394565.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	2 clinvar		3
missense			13 clinvar			13
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	14	2	0	16

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 45 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001394565.1	RefSeq	NP_001381494.1	9	MANE Select
ENST00000574428.6	Ensembl	ENSP00000459167.2	9	MANE Select
NM_001042546.2	RefSeq	NP_001036011.2	7	Standard
NM_001243728.1	RefSeq	NP_001230657.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

mitochondrial proton-transporting ATP synthase complex assembly

Molecular Function

protein binding

Cellular Component

mitochondrion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000576409
Coding exons: 9
Length: 41131
Individuals with no LoFs: 125735
Homozygous LoFs: 0
Heterozygous LoFs: 13
Defined: 125748
p: 0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.18	108	149	0.727	0.00000791	2233
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000071	0.000070	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.683

Gene Damage Prediction

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