PPP1R16B

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

Basic information

Region (hg38): 20:38805697-38923024

Links

ENSG00000101445 ∙ NCBI:26051 ∙ OMIM:613275 ∙ HGNC:15850 ∙ Uniprot:Q96T49 ∙ 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 PPP1R16B gene.

• not_specified (52 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP1R16B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015568.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			49	1		50
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	49	3	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP1R16B	protein_coding	protein_coding	ENST00000299824	10	117320

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000260	125475	0	1	125476	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.44	229	359	0.638	0.0000228	3698
Missense in Polyphen		66	142.42	0.46341		1495
Synonymous	1.93	123	153	0.802	0.0000105	1121
Loss of Function	4.73	1	28.0	0.0357	0.00000147	295

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000463	0.0000463
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulator of protein phosphatase 1 (PP1) that acts as a positive regulator of pulmonary endothelial cell (EC) barrier function (PubMed:18586956). Involved in the regulation of the PI3K/AKT signaling pathway, angiogenesis and endothelial cell proliferation (PubMed:25007873). Regulates angiogenesis and endothelial cell proliferation through the control of ECE1 dephosphorylation, trafficking and activity (By similarity). Protects the endothelial barrier from lipopolysaccharide (LPS)- induced vascular leakage (By similarity). Involved in the regulation of endothelial cell filopodia extension (By similarity). May be a downstream target for TGF-beta1 signaling cascade in endothelial cells (PubMed:16263087, PubMed:18586956). Involved in PKA-mediated moesin dephosphorylation which is important in EC barrier protection against thrombin stimulation (PubMed:18586956). Promotes the interaction of PPP1CA with RPSA/LAMR1 and in turn facilitates the dephosphorylation of RPSA/LAMR1 (PubMed:16263087). Involved in the dephosphorylation of EEF1A1 (PubMed:26497934). {ECO:0000250|UniProtKB:Q8VHQ3, ECO:0000250|UniProtKB:Q95N27, ECO:0000269|PubMed:16263087, ECO:0000269|PubMed:18586956, ECO:0000269|PubMed:25007873, ECO:0000269|PubMed:26497934}.

Intolerance Scores

• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.88

Haploinsufficiency Scores

• pHI: 0.631
• hipred: Y
• hipred_score: 0.775
• ghis: 0.497

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.219

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp1r16b
• Phenotype: normal phenotype

Gene ontology

• Biological process: positive regulation of endothelial cell proliferation;regulation of phosphatidylinositol 3-kinase signaling;regulation of protein dephosphorylation;positive regulation of protein dephosphorylation;negative regulation of protein dephosphorylation;regulation of phosphoprotein phosphatase activity;regulation of filopodium assembly;establishment of endothelial barrier;negative regulation of peptidyl-serine dephosphorylation;positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis
• Cellular component: nucleus;plasma membrane;nuclear speck;cell projection;perinuclear region of cytoplasm
• Molecular function: protein binding;protein phosphatase regulator activity