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.

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.

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				2	3	5
missense			56	4	5	65
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	56	6	8

Variants in PIF1

This is a list of pathogenic ClinVar variants found in the PIF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-64816333-C-G			Benign (Dec 31, 2019)
15-64816338-T-C		not specified	Uncertain significance (Oct 14, 2021)
15-64816348-C-T			Benign (Dec 31, 2019)
15-64816593-C-T		not specified	Likely benign (Aug 12, 2022)
15-64816594-G-A		not specified	Uncertain significance (Oct 12, 2021)
15-64816596-C-T			Benign (Jan 30, 2018)
15-64816610-G-T		not specified	Uncertain significance (May 20, 2024)
15-64816615-G-T		not specified	Uncertain significance (Oct 25, 2024)
15-64816623-C-T		not specified	Uncertain significance (Nov 18, 2022)
15-64816636-G-A		not specified	Uncertain significance (Dec 16, 2023)
15-64816639-C-T		not specified	Uncertain significance (Nov 27, 2023)
15-64816665-C-T			Benign (Jan 17, 2018)
15-64816683-C-T		not specified	Uncertain significance (Oct 05, 2023)
15-64816692-G-C		not specified	Uncertain significance (May 03, 2023)
15-64816728-C-T		not specified	Uncertain significance (Jan 19, 2024)
15-64816740-A-G		not specified	Uncertain significance (Jul 20, 2021)
15-64816743-T-G		not specified	Uncertain significance (Apr 12, 2024)
15-64816762-T-C		not specified	Uncertain significance (Oct 29, 2024)
15-64817999-G-A		not specified	Uncertain significance (Mar 26, 2024)
15-64818018-G-A			Likely benign (Dec 01, 2022)
15-64818037-C-T		not specified	Uncertain significance (Sep 17, 2021)
15-64818044-C-T		not specified	Uncertain significance (Sep 16, 2021)
15-64818068-A-G		not specified	Uncertain significance (Dec 06, 2024)
15-64818085-G-C		not specified	Uncertain significance (Feb 26, 2024)
15-64818285-C-T			Benign (Jun 26, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PIF1	protein_coding	protein_coding	ENST00000268043	12	10037

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.83e-16	0.0137	125588	0	160	125748	0.000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.312	297	313	0.950	0.0000185	3972
Missense in Polyphen		132	140.92	0.93669		1762
Synonymous	1.57	109	132	0.826	0.00000740	1425
Loss of Function	0.245	25	26.4	0.948	0.00000141	282

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00240	0.00239
Ashkenazi Jewish	0.00	0.00
East Asian	0.000927	0.000925
Finnish	0.00	0.00
European (Non-Finnish)	0.000507	0.000501
Middle Eastern	0.000927	0.000925
South Asian	0.000753	0.000752
Other	0.000163	0.000163

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

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

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