GeneBe

PIF1

PIF1 5'-to-3' DNA helicase, the group of DNA helicases

Basic information

Region (hg38): 15:64815632-64825668

Previous symbols: [ "C15orf20" ]

Links

ENSG00000140451 ∙ NCBI:80119 ∙ OMIM:610953 ∙ HGNC:26220 ∙ Uniprot:Q9H611 ∙ 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 PIF1 gene.

  • not_specified (123 variants)
  • not_provided (11 variants)
  • Recurrent_spontaneous_abortion (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIF1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001286496.2. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
3
clinvar
 6
missense
116
clinvar
7
clinvar
5
clinvar
 128
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 116 10 8
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PIF1protein_codingprotein_codingENST00000268043 1210037
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.83e-160.013712558801601257480.000636
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.3122973130.9500.00001853972
Missense in Polyphen132140.920.936691762
Synonymous1.571091320.8260.000007401425
Loss of Function0.2452526.40.9480.00000141282

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.002400.00239
Ashkenazi Jewish0.000.00
East Asian0.0009270.000925
Finnish0.000.00
European (Non-Finnish)0.0005070.000501
Middle Eastern0.0009270.000925
South Asian0.0007530.000752
Other0.0001630.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: DNA-dependent ATPase and 5'-3' DNA helicase required for the maintenance of both mitochondrial and nuclear genome stability. Efficiently unwinds G-quadruplex (G4) DNA structures and forked RNA-DNA hybrids. Resolves G4 structures, preventing replication pausing and double-strand breaks (DSBs) at G4 motifs. Involved in the maintenance of telomeric DNA. Inhibits telomere elongation, de novo telomere formation and telomere addition to DSBs via catalytic inhibition of telomerase. Reduces the processivity of telomerase by displacing active telomerase from DNA ends. Releases telomerase by unwinding the short telomerase RNA/telomeric DNA hybrid that is the intermediate in the telomerase reaction. Possesses an intrinsic strand annealing activity. {ECO:0000255|HAMAP-Rule:MF_03176, ECO:0000269|PubMed:16522649, ECO:0000269|PubMed:17172855, ECO:0000269|PubMed:17827721, ECO:0000269|PubMed:18835853, ECO:0000269|PubMed:19700773, ECO:0000269|PubMed:20524933, ECO:0000269|PubMed:23657261}.;
Pathway
Regulation of Telomerase (Consensus)

Recessive Scores

pRec
0.115

Intolerance Scores

loftool
0.864
rvis_EVS
0.56
rvis_percentile_EVS
81.67

Haploinsufficiency Scores

pHI
0.366
hipred
Y
hipred_score
0.515
ghis
0.543

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.191

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Pif1
Phenotype
normal phenotype; cellular phenotype;

Gene ontology

Biological process
mitochondrial genome maintenance;telomere maintenance;DNA replication;DNA repair;DNA recombination;regulation of telomere maintenance;negative regulation of telomere maintenance via telomerase;DNA duplex unwinding;negative regulation of telomerase activity
Cellular component
nuclear chromosome, telomeric region;replication fork;mitochondrion
Molecular function
magnesium ion binding;ATP binding;telomerase inhibitor activity;single-stranded DNA-dependent ATP-dependent DNA helicase activity;ATP-dependent 5'-3' DNA/RNA helicase activity;telomeric DNA binding;ATP-dependent 5'-3' DNA helicase activity;G-quadruplex DNA binding