PPP6R1

protein phosphatase 6 regulatory subunit 1, the group of MicroRNA protein coding host genes|Protein phosphatase 6 regulatory subunits

Basic information

Region (hg38): 19:55229779-55259017

Previous symbols: [ "KIAA1115", "SAPS1" ]

Links

ENSG00000105063 ∙ NCBI:22870 ∙ OMIM:610875 ∙ HGNC:29195 ∙ Uniprot:Q9UPN7 ∙ 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 PPP6R1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP6R1 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			67	2	1	70
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding					1	1
Total	0	0	67	2	2

Variants in PPP6R1

This is a list of pathogenic ClinVar variants found in the PPP6R1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-55230541-G-A			Benign (Jul 16, 2018)
19-55230622-G-A		not specified	Uncertain significance (Oct 09, 2024)
19-55230652-T-C		not specified	Uncertain significance (Dec 27, 2023)
19-55230661-G-A		not specified	Uncertain significance (Jun 03, 2022)
19-55230670-G-A		not specified	Uncertain significance (Dec 15, 2023)
19-55230816-C-T		not specified	Uncertain significance (Mar 31, 2023)
19-55230823-T-C		not specified	Uncertain significance (Jun 25, 2024)
19-55230847-C-T		not specified	Uncertain significance (Jul 09, 2021)
19-55230861-G-A		not specified	Uncertain significance (Aug 10, 2024)
19-55231426-G-A		not specified	Uncertain significance (Dec 14, 2023)
19-55231434-C-T		not specified	Uncertain significance (Dec 06, 2021)
19-55231441-C-T		not specified	Uncertain significance (Oct 29, 2021)
19-55231453-C-T		not specified	Uncertain significance (Jan 09, 2024)
19-55231461-T-C		not specified	Uncertain significance (Oct 11, 2024)
19-55231465-C-T		not specified	Uncertain significance (May 02, 2024)
19-55231473-A-G		not specified	Uncertain significance (Nov 17, 2023)
19-55231479-G-A		not specified	Uncertain significance (Jul 11, 2023)
19-55231482-T-C		not specified	Uncertain significance (Nov 10, 2024)
19-55231488-G-A		not specified	Uncertain significance (Jan 23, 2024)
19-55231613-C-T		not specified	Uncertain significance (May 31, 2023)
19-55231648-G-C		not specified	Uncertain significance (May 11, 2022)
19-55231821-G-A		not specified	Uncertain significance (Jan 29, 2024)
19-55231829-G-A		not specified	Uncertain significance (Apr 22, 2022)
19-55231829-G-C		not specified	Uncertain significance (Feb 10, 2022)
19-55231892-G-A		not specified	Uncertain significance (Dec 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP6R1	protein_coding	protein_coding	ENST00000412770	23	29216

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.983	0.0171	124588	0	13	124601	0.0000522

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0354	508	510	0.996	0.0000311	5677
Missense in Polyphen		136	182.15	0.74662		2107
Synonymous	-2.47	269	222	1.21	0.0000149	1733
Loss of Function	5.11	7	43.2	0.162	0.00000202	490

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000561	0.0000556
Finnish	0.000316	0.000278
European (Non-Finnish)	0.0000460	0.0000443
Middle Eastern	0.0000561	0.0000556
South Asian	0.0000349	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}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• rvis_EVS: 0.12
• rvis_percentile_EVS: 62.23

Haploinsufficiency Scores

• pHI: 0.165
• hipred: Y
• hipred_score: 0.771
• ghis: 0.500

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: Ppp6r1

Gene ontology

• Biological process: regulation of phosphoprotein phosphatase activity;COPII vesicle coating
• Cellular component: Golgi membrane;cytosol
• Molecular function: protein binding;Rho GTPase binding;protein phosphatase binding