ATP5IF1

ATP synthase inhibitory factor subunit 1, the group of Mitochondrial complex V: ATP synthase subunits

Basic information

Region (hg38): 1:28236109-28246906

Previous symbols: [ "ATPIF1" ]

Links

ENSG00000130770 ∙ NCBI:93974 ∙ OMIM:614981 ∙ HGNC:871 ∙ Uniprot:Q9UII2 ∙ 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 ATP5IF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP5IF1 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in ATP5IF1

This is a list of pathogenic ClinVar variants found in the ATP5IF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-28236230-G-T		not specified	Uncertain significance (Oct 27, 2022)
1-28236266-A-G		not specified	Uncertain significance (Jul 23, 2024)
1-28236443-G-A		not specified	Uncertain significance (Jun 28, 2022)
1-28237892-G-A		not specified	Uncertain significance (Jun 17, 2024)
1-28237970-G-T		not specified	Uncertain significance (Sep 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP5IF1	protein_coding	protein_coding	ENST00000335514	3	10798

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000104	0.374	125690	0	57	125747	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.119	67	64.3	1.04	0.00000336	691
Missense in Polyphen		14	18.238	0.76764		216
Synonymous	0.439	22	24.8	0.888	0.00000121	198
Loss of Function	0.0407	6	6.11	0.982	2.79e-7	57

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00126	0.00126
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000217	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.00000881	0.00000879
Middle Eastern	0.000217	0.000217
South Asian	0.000327	0.000327
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Endogenous F(1)F(o)-ATPase inhibitor limiting ATP depletion when the mitochondrial membrane potential falls below a threshold and the F(1)F(o)-ATP synthase starts hydrolyzing ATP to pump protons out of the mitochondrial matrix. Required to avoid the consumption of cellular ATP when the F(1)F(o)-ATP synthase enzyme acts as an ATP hydrolase. Indirectly acts as a regulator of heme synthesis in erythroid tissues: regulates heme synthesis by modulating the mitochondrial pH and redox potential, allowing FECH to efficiently catalyze the incorporation of iron into protoporphyrin IX to produce heme. {ECO:0000269|PubMed:12110673, ECO:0000269|PubMed:15528193, ECO:0000269|PubMed:19559621, ECO:0000269|PubMed:23135403}.
• Pathway: Electron Transport Chain (Consensus)

Recessive Scores

• pRec: 0.0967

Intolerance Scores

• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.76

Haploinsufficiency Scores

• pHI: 0.130
• hipred: N
• hipred_score: 0.372
• ghis: 0.607

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Atpif1
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: atp5if1a
• Affected structure: nucleate erythrocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: angiogenesis;negative regulation of endothelial cell proliferation;generation of precursor metabolites and energy;heme biosynthetic process;erythrocyte differentiation;negative regulation of ATPase activity;protein homooligomerization;protein homotetramerization;negative regulation of hydrolase activity;mitochondrial depolarization;reactive oxygen species metabolic process;positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway;positive regulation of proteolysis involved in cellular protein catabolic process;regulation of protein targeting to mitochondrion;regulation of ATP metabolic process;positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization
• Cellular component: mitochondrion;cell surface
• Molecular function: enzyme inhibitor activity;calmodulin binding;enzyme binding;ATPase inhibitor activity;protein homodimerization activity;angiostatin binding;ATPase binding;mitochondrial proton-transporting ATP synthase complex binding