PPP1R16A

protein phosphatase 1 regulatory subunit 16A, the group of Protein phosphatase 1 regulatory subunits|Ankyrin repeat domain containing|Myosin phosphatase targeting family

Basic information

Region (hg38): 8:144477969-144502121

Links

ENSG00000160972 ∙ NCBI:84988 ∙ OMIM:609172 ∙ HGNC:14941 ∙ Uniprot:Q96I34 ∙ 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 PPP1R16A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP1R16A 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			58	4		62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	58	5	0

Variants in PPP1R16A

This is a list of pathogenic ClinVar variants found in the PPP1R16A region.

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

Position	Type	Phenotype	Significance	ClinVar
8-144497201-G-A		not specified	Uncertain significance (Jul 15, 2021)
8-144497285-G-A		not specified	Uncertain significance (Nov 18, 2022)
8-144497333-A-G		not specified	Uncertain significance (Jan 26, 2022)
8-144497375-C-A		not specified	Uncertain significance (Jun 16, 2023)
8-144497379-G-A		not specified	Uncertain significance (Jul 02, 2024)
8-144497381-C-T		not specified	Uncertain significance (Mar 18, 2024)
8-144497429-G-A		not specified	Uncertain significance (Jun 07, 2024)
8-144498935-G-A		not specified	Uncertain significance (Jul 09, 2024)
8-144498970-A-G		not specified	Likely benign (Feb 27, 2024)
8-144499057-G-T		not specified	Uncertain significance (Jul 13, 2021)
8-144500119-A-G		not specified	Uncertain significance (Aug 21, 2024)
8-144500140-A-G		not specified	Uncertain significance (Mar 13, 2023)
8-144500171-C-A		not specified	Uncertain significance (Aug 23, 2021)
8-144500297-G-T		not specified	Uncertain significance (Oct 03, 2022)
8-144500302-G-C		not specified	Likely benign (Nov 18, 2022)
8-144500339-G-A		not specified	Uncertain significance (Aug 02, 2021)
8-144500356-G-A		not specified	Uncertain significance (Jan 23, 2024)
8-144500363-A-T		not specified	Uncertain significance (Feb 28, 2024)
8-144500526-G-A		not specified	Uncertain significance (Jun 02, 2023)
8-144500722-G-A		not specified	Uncertain significance (Jun 17, 2024)
8-144500851-G-C		not specified	Uncertain significance (Mar 20, 2023)
8-144500856-G-A		not specified	Uncertain significance (Sep 07, 2022)
8-144500880-G-A		not specified	Uncertain significance (Feb 08, 2025)
8-144500889-C-A		not specified	Uncertain significance (Aug 25, 2024)
8-144500898-G-A		not specified	Uncertain significance (Dec 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP1R16A	protein_coding	protein_coding	ENST00000292539	10	24153

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00439	0.994	125491	0	40	125531	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.128	320	327	0.980	0.0000197	3359
Missense in Polyphen		106	132.8	0.79818		1320
Synonymous	-2.97	193	147	1.31	0.00000946	1098
Loss of Function	2.81	8	22.3	0.358	0.00000126	218

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000931	0.0000907
Ashkenazi Jewish	0.00	0.00
East Asian	0.000175	0.000163
Finnish	0.0000504	0.0000462
European (Non-Finnish)	0.000266	0.000256
Middle Eastern	0.000175	0.000163
South Asian	0.000165	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits protein phosphatase 1 activity toward phosphorylase, myosin light chain and myosin substrates. {ECO:0000250}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.515
• rvis_EVS: -0.78
• rvis_percentile_EVS: 12.88

Haploinsufficiency Scores

• pHI: 0.161
• hipred: N
• hipred_score: 0.414
• ghis: 0.595

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.846

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp1r16a

Gene ontology

• Biological process: regulation of phosphoprotein phosphatase activity
• Cellular component: plasma membrane
• Molecular function: protein binding;protein phosphatase regulator activity