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.

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.

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				5		5
missense			51	7		58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	51	13	0

Variants in PPP6R2

This is a list of pathogenic ClinVar variants found in the PPP6R2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-50393999-G-A		not specified	Uncertain significance (Aug 14, 2024)
22-50394061-G-T		not specified	Uncertain significance (Aug 20, 2024)
22-50394095-C-G		not specified	Uncertain significance (Oct 27, 2023)
22-50406363-A-G		Charcot-Marie-Tooth disease type 4B3	Pathogenic (May 11, 2018)
22-50406747-C-G		not specified	Uncertain significance (Jan 10, 2022)
22-50406774-C-G		not specified	Uncertain significance (May 26, 2024)
22-50406865-A-G		not specified	Uncertain significance (Aug 19, 2024)
22-50414580-A-G		not specified	Uncertain significance (Oct 20, 2023)
22-50414609-G-A		not specified	Uncertain significance (May 14, 2024)
22-50414639-C-T		not specified	Uncertain significance (Oct 06, 2022)
22-50414660-C-T		not specified	Uncertain significance (Jan 18, 2023)
22-50418932-G-C		not specified	Uncertain significance (Jun 07, 2023)
22-50419395-C-T		not specified	Uncertain significance (Jan 03, 2024)
22-50419396-G-A		not specified	Likely benign (Sep 09, 2024)
22-50419399-C-T		not specified	Uncertain significance (Jun 26, 2024)
22-50419456-G-A		not specified	Uncertain significance (Nov 25, 2024)
22-50422318-G-A		not specified	Uncertain significance (Apr 25, 2022)
22-50423484-T-A		not specified	Uncertain significance (Mar 26, 2024)
22-50423484-T-C		not specified	Uncertain significance (Aug 12, 2021)
22-50423496-A-T		not specified	Uncertain significance (Aug 16, 2021)
22-50423535-T-G		not specified	Uncertain significance (Nov 23, 2021)
22-50423558-A-G		not specified	Uncertain significance (Dec 21, 2022)
22-50431258-G-A		not specified	Uncertain significance (Aug 19, 2024)
22-50431303-C-T		not specified	Uncertain significance (Aug 27, 2024)
22-50431306-C-T		not specified	Likely benign (Jan 23, 2024)

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