PPP1R14C

protein-coding

protein phosphatase 1 regulatory inhibitor subunit 14C, the group of Protein phosphatase 1 regulatory subunits

Gene summary

The degree of protein phosphorylation is regulated by a balance of protein kinase and phosphatase activities. Protein phosphatase-1 (PP1; see MIM 176875) is a signal-transducing phosphatase that influences neuronal activity, protein synthesis, metabolism, muscle contraction, and cell division. PPP1R14C is an inhibitor of PP1 (Liu et al., 2002 [PubMed 11812771]).[supplied by OMIM, Feb 2010]

MANE transcript

NM_030949.3

Inheritance

—

ClinVar variants

U:26

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr6:150,143,044-150,250,392

External References & Databases

Ensembl (ENSG00000198729)

Transcript & Mutation Effects

hg38 • Region Span ~107.3 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 PPP1R14C variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 25

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_030949.3. 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						0
missense			25 clinvar			25
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	26	0	0	26

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_030949.3	RefSeq	NP_112211.1	4	MANE Select
ENST00000361131.5	Ensembl	ENSP00000355260.4	4	MANE Select
ENST00000893449.1	Ensembl	ENSP00000563508.1	2	Standard
ENST00000893449.2	Ensembl	ENSP00000563508.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Glucocorticoid Receptor Pathway
Nuclear Receptors Meta-Pathway
Integrin-linked kinase signaling

Biological Process

negative regulation of phosphoprotein phosphatase activity
regulation of phosphorylation

Molecular Function

protein serine/threonine phosphatase inhibitor activity

Cellular Component

cytoplasm
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000361131
Coding exons: 4
Length: 107282
Individuals with no LoFs: 125697
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125703
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.670	63	79.9	0.789	0.00000375	1034
Missense (PolyPhen)		24	26.751	0.89716		349
Synonymous	-0.732	37	31.8	1.17	0.00000151	330
Loss of Function	0.920	5	7.77	0.644	3.31e-7	91

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000031	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000026	rare
South Asian	0.000069	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Inhibitor of the PP1 regulatory subunit PPP1CA.;

Recessive Scores

pRec: 0.0972

Intolerance Scores

LoFtool: 0.562
RVIS EVS: 0.04
RVIS percentile EVS: 56.25

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.478

Gene Damage Prediction

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