PPTC7

protein phosphatase targeting COQ7, the group of Protein phosphatases, Mg2+/Mn2+ dependent

Basic information

Region (hg38): 12:110533245-110583318

Links

ENSG00000196850 ∙ NCBI:160760 ∙ OMIM:609668 ∙ HGNC:30695 ∙ Uniprot:Q8NI37 ∙ 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 PPTC7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPTC7 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in PPTC7

This is a list of pathogenic ClinVar variants found in the PPTC7 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-110537054-C-T		not specified	Uncertain significance (Aug 30, 2021)
12-110538257-C-T		not specified	Uncertain significance (Jul 12, 2022)
12-110539863-T-G		not specified	Uncertain significance (Dec 20, 2021)
12-110545893-C-T		not specified	Uncertain significance (Sep 16, 2021)
12-110545982-C-T		not specified	Uncertain significance (Jan 22, 2025)
12-110551845-A-G		not specified	Uncertain significance (Dec 08, 2023)
12-110582950-C-T		not specified	Uncertain significance (Oct 27, 2022)
12-110582956-C-A		not specified	Uncertain significance (Jul 26, 2022)
12-110582991-G-A		not specified	Uncertain significance (Sep 27, 2024)
12-110583001-C-A		not specified	Uncertain significance (Jun 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPTC7	protein_coding	protein_coding	ENST00000354300	6	52006

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.938	0.0618	125740	0	4	125744	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.89	70	179	0.392	0.00000990	1954
Missense in Polyphen		9	66.559	0.13522		743
Synonymous	0.321	70	73.5	0.952	0.00000444	615
Loss of Function	3.12	1	13.2	0.0756	6.46e-7	164

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.163
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• pHI: 0.843
• hipred: Y
• hipred_score: 0.516
• ghis: 0.625

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.367

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pptc7

Gene ontology

• Biological process: protein dephosphorylation
• Cellular component: mitochondrion
• Molecular function: phosphoprotein phosphatase activity;metal ion binding