PPP6R1

protein-coding

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

Gene summary

Protein phosphatase regulatory subunits, such as SAPS1, modulate the activity of protein phosphatase catalytic subunits by restricting substrate specificity, recruiting substrates, and determining the intracellular localization of the holoenzyme. SAPS1 is a regulatory subunit for the protein phosphatase-6 catalytic subunit (PPP6C; MIM 612725) (Stefansson and Brautigan, 2006 [PubMed 16769727]).[supplied by OMIM, Nov 2010]

Previous symbols:

KIAA1115
SAPS1

MANE transcript

NM_014931.4

Inheritance

—

ClinVar variants

U:180B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.16

Max pathogenic AF

—

Genomic locus

chr19:55,229,779-55,259,017

External References & Databases

Ensembl (ENSG00000105063)

Transcript & Mutation Effects

hg38 • Region Span ~29.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PPP6R1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 158

not providedTotal: 9

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014931.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			5 clinvar	3 clinvar		8
missense			164 clinvar	4 clinvar	1 clinvar	169
nonsense			3 clinvar			3
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	180	7	1	188

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 100 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014931.4	RefSeq	NP_055746.3	23	MANE Select
ENST00000412770.7	Ensembl	ENSP00000414202.1	23	MANE Select
ENST00000587283.5	Ensembl	ENSP00000467521.1	23	Standard
ENST00000587283.6	Ensembl	ENSP00000467521.1	23	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vesicle-mediated transport
Membrane Trafficking
Post-translational protein modification
Metabolism of proteins
Transport to the Golgi and subsequent modification

Biological Process

regulation of phosphoprotein phosphatase activity
COPII vesicle coating

Molecular Function

protein binding
Rho GTPase binding
protein phosphatase binding

Cellular Component

Golgi membrane
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000412770
Coding exons: 23
Length: 29216
Individuals with no LoFs: 124588
Homozygous LoFs: 0
Heterozygous LoFs: 13
Defined: 124601
p: 0.0000522

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0354	508	510	0.996	0.0000311	5677
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000056	0.000056	rare
Finnish	0.00032	0.00028	rare
European (Non-Finnish)	0.000046	0.000044	rare
South Asian	0.000035	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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: 0.118

Intolerance Scores

RVIS EVS: 0.12
RVIS percentile EVS: 62.23

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.539

Gene Damage Prediction

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