PIFO

primary cilia formation

Basic information

Region (hg38): 1:111346599-111353013

Previous symbols: [ "C1orf88" ]

Links

ENSG00000173947 ∙ NCBI:128344 ∙ OMIM:614234 ∙ HGNC:27009 ∙ Uniprot:Q8TCI5 ∙ 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 PIFO gene.

• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIFO 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 PIFO

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

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

Position	Type	Phenotype	Significance	ClinVar
1-111346936-A-G		not specified	Uncertain significance (Sep 12, 2023)
1-111347713-A-G		not specified	Uncertain significance (Aug 08, 2023)
1-111348616-A-C		not specified	Uncertain significance (Jan 16, 2024)
1-111350123-C-T		not specified	Uncertain significance (Jan 23, 2024)
1-111350130-G-T		not specified	Uncertain significance (Jul 11, 2023)
1-111350150-C-G		not specified	Uncertain significance (Oct 12, 2021)
1-111350158-A-G		not specified	Uncertain significance (Jan 06, 2023)
1-111351292-A-G		not specified	Uncertain significance (Feb 16, 2023)
1-111351295-C-T		not specified	Uncertain significance (Feb 06, 2023)
1-111351296-G-A		not specified	Uncertain significance (Dec 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PIFO	protein_coding	protein_coding	ENST00000369738	6	6726

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.94e-8	0.174	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.458	88	101	0.872	0.00000481	1245
Missense in Polyphen		35	40.279	0.86894		510
Synonymous	0.0683	35	35.5	0.985	0.00000171	348
Loss of Function	0.0926	11	11.3	0.970	5.42e-7	138

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000276	0.000276
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000267	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.000163	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: During primary cilia disassembly, involved in cilia disassembly. Required specifically to control cilia retraction as well as the liberation and duplication of the basal body/centrosome. May act by stimulating AURKA activity at the basal body in a cell cycle-dependent manner. {ECO:0000269|PubMed:20643351}.

Intolerance Scores

• rvis_EVS: 0.3
• rvis_percentile_EVS: 72.01

Haploinsufficiency Scores

• pHI: 0.0534
• hipred: N
• hipred_score: 0.144
• ghis: 0.390

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pifo
• Phenotype: reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); embryo phenotype; cellular phenotype

Gene ontology

• Biological process: cell projection organization;regulation of cell projection organization;positive regulation of kinase activity
• Cellular component: nucleus;trans-Golgi network;cytoplasmic vesicle;ciliary basal body
• Molecular function: protein binding;Rab GTPase binding;kinesin binding;protein kinase binding;gamma-tubulin binding;beta-tubulin binding