PPP6R2

protein phosphatase 6 regulatory subunit 2, the group of Armadillo like helical domain containing|Protein phosphatase 6 regulatory subunits

Basic information

Region (hg38): 22:50343304-50445090

Previous symbols: [ "KIAA0685", "SAPS2" ]

Links

ENSG00000100239 ∙ NCBI:9701 ∙ OMIM:610877 ∙ HGNC:19253 ∙ Uniprot:O75170 ∙ 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 PPP6R2 gene.

• not_specified (145 variants)
• not_provided (9 variants)
• Prostate_cancer (1 variants)
• Charcot-Marie-Tooth_disease_type_4B3 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP6R2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001242898.2. 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				6		6
missense			135	12		147
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	135	18	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP6R2	protein_coding	protein_coding	ENST00000395741	21	101782

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.164	0.836	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.934	514	577	0.891	0.0000357	6093
Missense in Polyphen		113	183.38	0.61621		2168
Synonymous	-0.527	262	251	1.04	0.0000178	1861
Loss of Function	4.51	10	41.3	0.242	0.00000203	471

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000153	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000110	0.000105
Middle Eastern	0.000109	0.000109
South Asian	0.0000332	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulatory subunit of protein phosphatase 6 (PP6). May function as a scaffolding PP6 subunit. Involved in the PP6- mediated dephosphorylation of NFKBIE opposing its degradation in response to TNF-alpha. {ECO:0000269|PubMed:16769727}.

Recessive Scores

• pRec: 0.0893

Intolerance Scores

• rvis_EVS: 0.7
• rvis_percentile_EVS: 85.31

Haploinsufficiency Scores

• pHI: 0.161
• hipred: Y
• hipred_score: 0.693
• ghis: 0.576

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp6r2
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Cellular component: cytosol;intracellular membrane-bounded organelle
• Molecular function: protein binding