PPP1R17

protein phosphatase 1 regulatory subunit 17, the group of Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 7:31687215-31708455

Previous symbols: [ "C7orf16" ]

Links

ENSG00000106341 ∙ NCBI:10842 ∙ OMIM:604088 ∙ HGNC:16973 ∙ Uniprot:O96001 ∙ 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 PPP1R17 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP1R17 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			6	1	1	8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	1

Variants in PPP1R17

This is a list of pathogenic ClinVar variants found in the PPP1R17 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-31692470-T-G		not specified	Benign (Mar 29, 2016)
7-31692491-T-C		not specified	Uncertain significance (May 17, 2023)
7-31692494-A-G		not specified	Uncertain significance (Apr 19, 2024)
7-31692504-C-A		not specified	Uncertain significance (Jan 31, 2022)
7-31695495-G-A		not specified	Uncertain significance (Aug 29, 2024)
7-31695526-G-A		not specified	Uncertain significance (Nov 09, 2024)
7-31695555-G-A		Hypercholesterolemia	Uncertain significance (Aug 03, 2023)
7-31695572-A-C		not specified	Uncertain significance (Jun 24, 2022)
7-31695619-C-T		not specified	Uncertain significance (Dec 15, 2022)
7-31696988-A-G		not specified	Uncertain significance (Mar 29, 2024)
7-31697032-C-G		not specified	Uncertain significance (Dec 20, 2021)
7-31697039-C-A		not specified	Uncertain significance (Sep 26, 2024)
7-31697087-C-T		not specified	Uncertain significance (May 26, 2024)
7-31697103-C-T		not specified	Uncertain significance (Nov 10, 2024)
7-31707216-T-C		not specified	Uncertain significance (Oct 25, 2023)
7-31707242-G-A		not specified	Likely benign (Dec 04, 2023)
7-31707253-C-A		not specified	Uncertain significance (Apr 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP1R17	protein_coding	protein_coding	ENST00000342032	4	21741

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00105	0.618	125645	0	98	125743	0.000390

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0203	85	84.5	1.01	0.00000414	1027
Missense in Polyphen		23	25.445	0.9039		319
Synonymous	0.0244	30	30.2	0.994	0.00000163	277
Loss of Function	0.558	5	6.54	0.764	2.74e-7	89

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00104	0.00103
Ashkenazi Jewish	0.00423	0.00418
East Asian	0.0000544	0.0000544
Finnish	0.0000468	0.0000462
European (Non-Finnish)	0.000134	0.000132
Middle Eastern	0.0000544	0.0000544
South Asian	0.000166	0.000163
Other	0.00101	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits phosphatase activities of protein phosphatase 1 (PP1) and protein phosphatase 2A (PP2A) complexes. {ECO:0000250}.
• Pathway: Long-term depression - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.194

Intolerance Scores

• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.66

Haploinsufficiency Scores

• pHI: 0.689
• hipred: N
• hipred_score: 0.428
• ghis: 0.479

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: Ppp1r17

Gene ontology

• Biological process: central nervous system development;regulation of phosphatase activity;negative regulation of phosphoprotein phosphatase activity;intracellular signal transduction
• Cellular component: cellular_component;nucleoplasm
• Molecular function: protein serine/threonine phosphatase inhibitor activity