PPP1R42

protein phosphatase 1 regulatory subunit 42, the group of Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 8:66964099-67056604

Previous symbols: [ "LRRC67" ]

Links

ENSG00000178125 ∙ NCBI:286187 ∙ OMIM:617720 ∙ HGNC:33732 ∙ Uniprot:Q7Z4L9 ∙ 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 PPP1R42 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP1R42 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in PPP1R42

This is a list of pathogenic ClinVar variants found in the PPP1R42 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-66988474-A-G		not specified	Uncertain significance (Jan 16, 2024)
8-67010734-T-C		not specified	Uncertain significance (Oct 20, 2023)
8-67013026-C-T		not specified	Uncertain significance (May 20, 2024)
8-67014510-G-T		not specified	Uncertain significance (Jul 12, 2022)
8-67017692-T-A		not specified	Uncertain significance (Nov 15, 2021)
8-67045822-T-C		not specified	Uncertain significance (Nov 10, 2022)
8-67045895-C-A		not specified	Uncertain significance (Jan 11, 2023)
8-67051247-A-T		not specified	Uncertain significance (Dec 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP1R42	protein_coding	protein_coding	ENST00000324682	5	92506

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000174	0.457	125354	2	358	125714	0.00143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	74	103	0.719	0.00000458	1470
Missense in Polyphen		15	25.849	0.58028		400
Synonymous	-0.165	42	40.7	1.03	0.00000184	432
Loss of Function	0.484	8	9.62	0.832	5.45e-7	136

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00171	0.00169
Ashkenazi Jewish	0.00182	0.00179
East Asian	0.0000584	0.0000544
Finnish	0.00103	0.00102
European (Non-Finnish)	0.00238	0.00231
Middle Eastern	0.0000584	0.0000544
South Asian	0.000351	0.000294
Other	0.000685	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates phosphatase activity of protein phosphatase 1 (PP1) complexes in the testis. {ECO:0000250|UniProtKB:Q8R1Z4}.

Intolerance Scores

• rvis_EVS: 0.37
• rvis_percentile_EVS: 74.95

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.398

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp1r42
• Phenotype: skeleton phenotype

Gene ontology

• Biological process: regulation of phosphatase activity
• Cellular component: manchette;cytoplasm;centrosome;microtubule organizing center;microtubule cytoskeleton
• Molecular function: actin binding;tubulin binding;dynein complex binding