PDF

peptide deformylase, mitochondrial

Basic information

Region (hg38): 16:69326913-69330588

Links

ENSG00000258429 ∙ NCBI:64146 ∙ OMIM:618720 ∙ HGNC:30012 ∙ Uniprot:Q9HBH1 ∙ 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 PDF gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDF 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				1	1	2
missense			33	1	1	35
nonsense			2			2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			5		2	7
Total	0	0	40	2	4

Variants in PDF

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

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

Position	Type	Phenotype	Significance	ClinVar
16-69328638-C-A		COG8-congenital disorder of glycosylation	Uncertain significance (Jan 12, 2018)
16-69328700-G-A		COG8-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
16-69328714-G-A		COG8-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
16-69328804-T-C		COG8-congenital disorder of glycosylation	Uncertain significance (Jan 12, 2018)
16-69328874-T-A		COG8-congenital disorder of glycosylation	Benign (Jan 12, 2018)
16-69328876-C-A		COG8-congenital disorder of glycosylation	Benign (Jan 12, 2018)
16-69329009-C-CA		Congenital disorder of glycosylation	Uncertain significance (Jun 14, 2016)
16-69329053-G-A		not specified	Uncertain significance (Apr 04, 2024)
16-69329066-T-G		not specified	Uncertain significance (May 09, 2024)
16-69329070-C-T		not specified	Uncertain significance (Jun 05, 2023)
16-69329133-C-T		COG8-congenital disorder of glycosylation	Uncertain significance (Jan 12, 2018)
16-69329138-C-G		not specified	Uncertain significance (Jan 03, 2024)
16-69329167-T-A		not specified	Uncertain significance (Jul 09, 2021)
16-69329171-G-A		not specified	Uncertain significance (Jun 29, 2023)
16-69329186-AG-A		not specified	Likely benign (Dec 14, 2016)
16-69330079-G-A			Benign (Oct 01, 2024)
16-69330099-G-C		not specified	Uncertain significance (Aug 27, 2024)
16-69330117-C-T		not specified	Uncertain significance (Oct 19, 2024)
16-69330128-A-C		not specified	Uncertain significance (Mar 16, 2024)
16-69330131-G-A		not specified	Uncertain significance (Dec 21, 2022)
16-69330136-C-T		not specified	Uncertain significance (Nov 13, 2024)
16-69330164-G-A		not specified	Uncertain significance (Feb 05, 2024)
16-69330165-G-A		not specified	Uncertain significance (Dec 03, 2024)
16-69330182-G-T		not specified	Uncertain significance (Nov 26, 2024)
16-69330200-G-A		not specified	Uncertain significance (Jun 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDF	protein_coding	protein_coding	ENST00000288022	2	1975

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000587	0.150	123444	0	12	123456	0.0000486

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.19	123	91.1	1.35	0.00000461	1479
Missense in Polyphen		34	31.898	1.0659		455
Synonymous	-3.46	69	40.8	1.69	0.00000231	521
Loss of Function	-0.695	7	5.28	1.33	2.30e-7	63

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000155	0.000153
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000548	0.0000541
Middle Eastern	0.00	0.00
South Asian	0.0000999	0.0000987
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Removes the formyl group from the N-terminal Met of newly synthesized proteins. {ECO:0000250}.

Haploinsufficiency Scores

• pHI: 0.0688
• hipred: N
• hipred_score: 0.244
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdf

Gene ontology

• Biological process: translation;positive regulation of cell population proliferation;peptidyl-methionine modification;N-terminal protein amino acid modification;co-translational protein modification
• Cellular component: mitochondrion
• Molecular function: peptide deformylase activity;metal ion binding