PPP1R14D

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

Basic information

Region (hg38): 15:40815450-40828709

Links

ENSG00000166143 ∙ NCBI:54866 ∙ OMIM:613256 ∙ HGNC:14953 ∙ Uniprot:Q9NXH3 ∙ 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 PPP1R14D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP1R14D 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			8	2		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	2	0

Variants in PPP1R14D

This is a list of pathogenic ClinVar variants found in the PPP1R14D region.

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

Position	Type	Phenotype	Significance	ClinVar
15-40815686-T-G		not specified	Uncertain significance (Dec 16, 2022)
15-40815709-C-T		not specified	Uncertain significance (Mar 16, 2024)
15-40815728-T-C		not specified	Likely benign (May 30, 2024)
15-40815973-G-A		not specified	Likely benign (Feb 26, 2024)
15-40816188-C-T		not specified	Likely benign (Dec 20, 2023)
15-40816205-C-A		not specified	Uncertain significance (Sep 26, 2023)
15-40828411-A-T		not specified	Uncertain significance (Jun 06, 2023)
15-40828439-C-A		not specified	Uncertain significance (May 17, 2023)
15-40828452-C-A		not specified	Uncertain significance (May 03, 2023)
15-40828454-C-T		not specified	Uncertain significance (Apr 22, 2024)
15-40828499-A-G		not specified	Uncertain significance (Feb 02, 2024)
15-40828508-G-C		not specified	Uncertain significance (Oct 12, 2021)
15-40828535-T-C		not specified	Uncertain significance (Apr 26, 2024)
15-40828579-C-G		not specified	Uncertain significance (Mar 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP1R14D	protein_coding	protein_coding	ENST00000427255	5	13258

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000239	0.303	125730	0	6	125736	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.207	90	95.7	0.941	0.00000522	1251
Missense in Polyphen		7	9.7715	0.71637		125
Synonymous	1.60	27	39.8	0.678	0.00000211	416
Loss of Function	0.242	9	9.82	0.917	4.52e-7	119

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000377	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibitor of PPP1CA. Has inhibitory activity only when phosphorylated, creating a molecular switch for regulating the phosphorylation status of PPP1CA substrates and smooth muscle contraction. {ECO:0000269|PubMed:12974676}.

Intolerance Scores

• loftool: 0.148
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.33

Haploinsufficiency Scores

• pHI: 0.191
• hipred: N
• hipred_score: 0.123
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0494

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp1r14d
• Phenotype: muscle phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of phosphorylation;negative regulation of protein serine/threonine phosphatase activity;positive regulation of protein serine/threonine phosphatase activity
• Cellular component: cytoplasm
• Molecular function: protein serine/threonine phosphatase inhibitor activity