PPP6C

protein phosphatase 6 catalytic subunit, the group of Protein phosphatase catalytic subunits

Basic information

Region (hg38): 9:125146573-125189939

Links

ENSG00000119414 ∙ NCBI:5537 ∙ OMIM:612725 ∙ HGNC:9323 ∙ Uniprot:O00743 ∙ 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 PPP6C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP6C 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
missense			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	6	0	1

Variants in PPP6C

This is a list of pathogenic ClinVar variants found in the PPP6C region.

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

Position	Type	Phenotype	Significance	ClinVar
9-125149695-G-A		not specified	Uncertain significance (Aug 26, 2024)
9-125149801-G-A		Malignant melanoma of skin • Squamous cell lung carcinoma	Likely pathogenic (May 31, 2016)
9-125149898-T-A		not specified	Uncertain significance (Oct 08, 2024)
9-125153593-A-G			Benign (Jul 06, 2018)
9-125153700-G-C		not specified	Uncertain significance (Dec 05, 2024)
9-125158346-T-C		not specified	Uncertain significance (May 30, 2024)
9-125160897-G-C		not specified	Uncertain significance (Dec 28, 2022)
9-125189564-G-A		not specified	Likely benign (Aug 12, 2024)
9-125189577-G-A		not specified	Uncertain significance (Dec 05, 2022)
9-125189579-G-A		not specified	Uncertain significance (Jun 02, 2023)
9-125189597-G-C		not specified	Uncertain significance (Apr 23, 2024)
9-125189693-T-C		not specified	Uncertain significance (Feb 10, 2022)
9-125189698-G-C		not specified	Uncertain significance (Jun 21, 2021)
9-125189704-G-T		not specified	Uncertain significance (Dec 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP6C	protein_coding	protein_coding	ENST00000451402	8	43367

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.855	0.145	125558	1	184	125743	0.000736

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.58	93	194	0.479	0.0000101	2218
Missense in Polyphen		24	78.479	0.30582		945
Synonymous	-0.568	75	69.0	1.09	0.00000346	665
Loss of Function	3.47	3	19.5	0.154	0.00000106	224

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000663	0.0000663
Ashkenazi Jewish	0.00	0.00
East Asian	0.00815	0.00731
Finnish	0.00	0.00
European (Non-Finnish)	0.0000853	0.0000791
Middle Eastern	0.00815	0.00731
South Asian	0.00133	0.00127
Other	0.000170	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalytic subunit of protein phosphatase 6 (PP6). PP6 is a component of a signaling pathway regulating cell cycle progression in response to IL2 receptor stimulation. N-terminal domain restricts G1 to S phase progression in cancer cells, in part through control of cyclin D1. Downregulates MAP3K7 kinase activation of the IL1 signaling pathway by dephosphorylation of MAP3K7. Participates also in the innate immune defense against viruses by desphosphorylating RIG-I/DDX58, an essential step that triggers RIG-I/DDX58-mediated signaling activation. {ECO:0000269|PubMed:10227379, ECO:0000269|PubMed:17079228, ECO:0000269|PubMed:17568194, ECO:0000269|PubMed:29053956, ECO:0000269|PubMed:9013334}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;IL1;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;TNFalpha;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport (Consensus)

Recessive Scores

• pRec: 0.338

Intolerance Scores

• loftool: 0.272
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.75

Haploinsufficiency Scores

• pHI: 0.570
• hipred: Y
• hipred_score: 0.714
• ghis: 0.608

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.584

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp6c
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; embryo 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); neoplasm; immune system phenotype

Gene ontology

• Biological process: G1/S transition of mitotic cell cycle;protein dephosphorylation;innate immune response;COPII vesicle coating
• Cellular component: Golgi membrane;mitochondrion;cytosol
• Molecular function: protein serine/threonine phosphatase activity;protein binding;metal ion binding