PPP1R10

protein phosphatase 1 regulatory subunit 10, the group of Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 6:30600412-30618612

Links

ENSG00000204569 ∙ NCBI:5514 ∙ OMIM:603771 ∙ HGNC:9284 ∙ Uniprot:Q96QC0 ∙ 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 PPP1R10 gene.

• Inborn genetic diseases (31 variants)
• not provided (5 variants)
• Delayed speech and language development;Generalized muscle weakness;Intellectual disability, moderate;Abnormal facial shape (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP1R10 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	2	3
missense			29	3		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region					1	1
non coding						0
Total	0	0	30	4	2

Variants in PPP1R10

This is a list of pathogenic ClinVar variants found in the PPP1R10 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-30601655-A-G		not specified	Uncertain significance (Jun 29, 2023)
6-30601965-C-T		not specified	Uncertain significance (Aug 21, 2023)
6-30602025-G-A		not specified	Uncertain significance (Apr 07, 2022)
6-30602043-C-T		not specified	Uncertain significance (May 09, 2023)
6-30602065-G-A		not specified	Uncertain significance (Dec 28, 2022)
6-30602071-G-A		not specified	Uncertain significance (Mar 07, 2023)
6-30602227-T-G		not specified	Uncertain significance (Dec 14, 2023)
6-30602241-G-A		not specified	Uncertain significance (Aug 13, 2021)
6-30602293-C-A		not specified	Uncertain significance (Feb 02, 2022)
6-30602335-C-G		not specified	Uncertain significance (Sep 26, 2023)
6-30602374-C-T		not specified	Uncertain significance (May 23, 2023)
6-30602466-C-A		not specified	Uncertain significance (Dec 19, 2022)
6-30602566-C-G		not specified	Uncertain significance (Feb 13, 2024)
6-30602571-C-A		not specified	Uncertain significance (May 11, 2022)
6-30602597-G-A			Benign (Aug 16, 2019)
6-30602601-G-A		not specified	Uncertain significance (May 05, 2023)
6-30602634-G-A		not specified	Uncertain significance (May 03, 2023)
6-30602635-G-A		not specified	Uncertain significance (Jul 09, 2021)
6-30602942-C-T		not specified	Uncertain significance (Aug 10, 2021)
6-30603245-T-G		not specified	Uncertain significance (Sep 27, 2021)
6-30603269-T-C		not specified	Uncertain significance (Jan 04, 2024)
6-30603512-C-G		not specified	Likely benign (Jun 24, 2022)
6-30603783-A-C		not specified	Uncertain significance (Jul 08, 2022)
6-30604068-C-T		not specified	Uncertain significance (Sep 29, 2023)
6-30604080-T-C		not specified	Uncertain significance (Dec 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP1R10	protein_coding	protein_coding	ENST00000376511	18	18213

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000162	125743	0	4	125747	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.95	377	576	0.654	0.0000340	6028
Missense in Polyphen		51	117.03	0.43577		1494
Synonymous	0.268	202	207	0.976	0.0000121	1990
Loss of Function	6.19	3	50.4	0.0595	0.00000365	492

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000647	0.0000615
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Scaffold protein which mediates the formation of the PTW/PP1 phosphatase complex by providing a binding platform to each component of the complex. The PTW/PP1 phosphatase complex plays a role in the control of chromatin structure and cell cycle progression during the transition from mitosis into interphase. Mediates interaction of WDR82 and PPP1CA. Inhibitor of PPP1CA and PPP1CC phosphatase activities. Has inhibitory activity on PPP1CA only when phosphorylated. Binds to mRNA, single-stranded DNA (ssDNA), poly(A) and poly(G) homopolymers (By similarity). {ECO:0000250, ECO:0000269|PubMed:9450550}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.114
• rvis_EVS: -0.78
• rvis_percentile_EVS: 12.97

Haploinsufficiency Scores

• pHI: 0.438
• hipred: Y
• hipred_score: 0.701
• ghis: 0.496

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp1r10
• 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)

Zebrafish Information Network

• Gene name: ppp1r10
• Affected structure: eye
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: protein import into nucleus;negative regulation of cardiac muscle cell apoptotic process;positive regulation of telomere maintenance;negative regulation of phosphoprotein phosphatase activity;negative regulation of mitotic DNA damage checkpoint
• Cellular component: nuclear chromosome, telomeric region;chromatin;nucleus;nucleoplasm;nuclear body;PTW/PP1 phosphatase complex
• Molecular function: DNA binding;RNA binding;protein phosphatase inhibitor activity;protein binding;metal ion binding