PPP1R16A

protein-coding

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

Gene summary

Myosin light chain kinase and phosphatase (MLCP) complexes control the phosphorylation states of regulatory myosin light chains, which is crucial for muscle and intracellular movement. MLCPs typically contain a catalytic protein phosphatase 1 (PP1c) subunit, a myosin phosphatase targeting (MYPT) subunit, and another smaller subunit. The protein encoded by this gene represents an MYPT subunit, which is responsible for directing PP1c to its intended targets. However, while the phosphorylation of other MYPT members results in PP1c inactivation, phosphorylation of the encoded protein by protein kinase A results in PP1c activation. [provided by RefSeq, Jan 2020]

MANE transcript

NM_001329443.2

Inheritance

—

ClinVar variants

U:103B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.36

Max pathogenic AF

—

Genomic locus

chr8:144,477,969-144,502,121

External References & Databases

Ensembl (ENSG00000160972)

Transcript & Mutation Effects

hg38 • Region Span ~24.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PPP1R16A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 106

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001329443.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			102 clinvar	6 clinvar		108
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	103	8	0	111

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 109 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001329443.2	RefSeq	NP_001316372.1	10	MANE Select
ENST00000435887.2	Ensembl	ENSP00000391126.1	10	MANE Select
NM_001329442.2	RefSeq	NP_001316371.1	10	Standard
NM_001329444.2	RefSeq	NP_001316373.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of phosphoprotein phosphatase activity

Molecular Function

protein binding
protein phosphatase regulator activity

Cellular Component

plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000292539
Coding exons: 10
Length: 24153
Individuals with no LoFs: 125491
Homozygous LoFs: 0
Heterozygous LoFs: 40
Defined: 125531
p: 0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.128	320	327	0.980	0.0000197	3359
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000064	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00018	0.00016	rare
Finnish	0.000050	0.000046	rare
European (Non-Finnish)	0.00027	0.00026	rare
South Asian	0.00017	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.846

Gene Damage Prediction

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