PPDPF

pancreatic progenitor cell differentiation and proliferation factor

Basic information

Region (hg38): 20:63520754-63527076

Previous symbols: [ "C20orf149" ]

Links

ENSG00000125534 ∙ NCBI:79144 ∙ ∙ HGNC:16142 ∙ Uniprot:Q9H3Y8 ∙ 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 PPDPF gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPDPF 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			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	0	0

Variants in PPDPF

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

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

Position	Type	Phenotype	Significance	ClinVar
20-63521321-C-T		not specified	Uncertain significance (Jul 09, 2021)
20-63521348-C-A		not specified	Uncertain significance (Sep 17, 2021)
20-63521515-G-A		not specified	Uncertain significance (Aug 21, 2023)
20-63521515-G-T		not specified	Uncertain significance (Apr 03, 2023)
20-63521545-G-A		not specified	Uncertain significance (Nov 25, 2024)
20-63521673-C-T		not specified	Uncertain significance (Sep 22, 2023)
20-63521674-C-T		not specified	Uncertain significance (Nov 20, 2024)
20-63521677-A-G		not specified	Uncertain significance (Mar 08, 2024)
20-63521691-C-T		not specified	Uncertain significance (Oct 01, 2024)
20-63521706-T-G		not specified	Uncertain significance (Dec 07, 2024)
20-63521727-C-T		not specified	Uncertain significance (Dec 03, 2024)
20-63521795-G-T		not specified	Uncertain significance (Mar 26, 2024)
20-63521799-G-C		not specified	Uncertain significance (Dec 22, 2023)
20-63521812-C-T		not specified	Uncertain significance (Jul 14, 2022)
20-63521815-G-T		not specified	Uncertain significance (Apr 18, 2023)
20-63521824-C-G		not specified	Uncertain significance (Mar 13, 2023)
20-63521851-G-A		not specified	Uncertain significance (Feb 28, 2024)
20-63521852-C-A		not specified	Uncertain significance (Mar 14, 2025)
20-63521856-G-C		not specified	Uncertain significance (Sep 24, 2024)
20-63521857-C-G		not specified	Uncertain significance (Dec 01, 2022)
20-63521868-C-A		not specified	Uncertain significance (Oct 05, 2023)
20-63521871-C-T		not specified	Uncertain significance (Sep 16, 2021)
20-63521874-T-A		not specified	Uncertain significance (Dec 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPDPF	protein_coding	protein_coding	ENST00000370179	3	1483

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000102	0.211	125399	0	9	125408	0.0000359

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.368	82	73.1	1.12	0.00000369	731
Missense in Polyphen		17	13.232	1.2847		175
Synonymous	-1.80	42	29.5	1.42	0.00000158	229
Loss of Function	-0.943	5	3.18	1.57	1.44e-7	33

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000286	0.0000265
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable regulator of exocrine pancreas development. {ECO:0000250}.

Intolerance Scores

• loftool: 0.455
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.0793
• hipred: N
• hipred_score: 0.170
• ghis: 0.553

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• 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: Ppdpf

Zebrafish Information Network

• Gene name: ppdpfa
• Affected structure: exocrine pancreas
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: multicellular organism development;cell differentiation