PPP1R12C

protein phosphatase 1 regulatory subunit 12C, the group of Protein phosphatase 1 regulatory subunits|Myosin phosphatase targeting family|Ankyrin repeat domain containing

Basic information

Region (hg38): 19:55090914-55117637

Previous symbols: [ "LENG3" ]

Links

ENSG00000125503 ∙ NCBI:54776 ∙ OMIM:613245 ∙ HGNC:14947 ∙ Uniprot:Q9BZL4 ∙ 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 PPP1R12C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP1R12C 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				6	2	8
missense			64	3	1	68
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	64	9	3

Variants in PPP1R12C

This is a list of pathogenic ClinVar variants found in the PPP1R12C region.

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

Position	Type	Phenotype	Significance	ClinVar
19-55091485-T-C		not specified	Uncertain significance (Mar 09, 2025)
19-55091496-G-A			Likely benign (Sep 01, 2022)
19-55091540-C-T		not specified	Uncertain significance (Jan 18, 2022)
19-55091542-C-A		not specified	Uncertain significance (May 23, 2023)
19-55091542-C-T		not specified	Uncertain significance (Jun 11, 2021)
19-55091549-C-T		not specified	Uncertain significance (Jan 24, 2025)
19-55091658-C-T		not specified	Uncertain significance (Apr 29, 2024)
19-55091681-C-A		not specified	Uncertain significance (Jun 22, 2023)
19-55091691-C-A		not specified	Uncertain significance (Oct 20, 2023)
19-55091894-C-A		not specified	Uncertain significance (Feb 06, 2024)
19-55092253-T-G		not specified	Uncertain significance (Dec 13, 2022)
19-55092290-G-A		not specified	Uncertain significance (Nov 09, 2024)
19-55092293-G-A		not specified	Uncertain significance (Feb 13, 2025)
19-55092297-C-G		not specified	Uncertain significance (Apr 23, 2024)
19-55092299-C-T		not specified	Uncertain significance (Jun 29, 2023)
19-55092301-T-C		not specified	Uncertain significance (Apr 18, 2023)
19-55092500-C-T		not specified	Uncertain significance (Jul 09, 2021)
19-55092543-T-A		not specified	Uncertain significance (Dec 01, 2022)
19-55092637-C-A		not specified	Uncertain significance (Mar 12, 2024)
19-55092638-G-C		not specified	Uncertain significance (Dec 08, 2021)
19-55092803-C-T		not specified	Uncertain significance (Aug 05, 2024)
19-55092819-G-C		not specified	Uncertain significance (Sep 26, 2023)
19-55092832-G-A		not specified	Uncertain significance (Jul 05, 2023)
19-55092854-C-T		not specified	Uncertain significance (Sep 01, 2024)
19-55092855-G-A		not specified	Likely benign (Feb 21, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP1R12C	protein_coding	protein_coding	ENST00000263433	22	26647

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0867	0.913	125733	0	14	125747	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.63	343	439	0.781	0.0000306	4858
Missense in Polyphen		177	247.68	0.71463		2465
Synonymous	-0.427	198	191	1.04	0.0000136	1659
Loss of Function	4.34	10	39.3	0.254	0.00000210	449

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000931	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.000173	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.000173	0.000163
South Asian	0.000204	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates myosin phosphatase activity. {ECO:0000269|PubMed:11399775}.
• Pathway: Focal adhesion - Homo sapiens (human);Oxytocin signaling pathway - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Vascular smooth muscle contraction - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);Focal Adhesion (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.525
• rvis_EVS: -1.04
• rvis_percentile_EVS: 7.83

Haploinsufficiency Scores

• pHI: 0.291
• hipred: Y
• hipred_score: 0.731
• ghis: 0.602

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp1r12c

Gene ontology

• Biological process: signal transduction;negative regulation of catalytic activity
• Cellular component: cytoplasm;cytoskeleton
• Molecular function: enzyme inhibitor activity;protein binding;phosphatase regulator activity;protein kinase binding