PPP6R3

protein phosphatase 6 regulatory subunit 3, the group of Protein phosphatase 6 regulatory subunits|Armadillo like helical domain containing

Basic information

Region (hg38): 11:68460731-68615334

Previous symbols: [ "C11orf23", "SAPS3" ]

Links

ENSG00000110075 ∙ NCBI:55291 ∙ OMIM:610879 ∙ HGNC:1173 ∙ Uniprot:Q5H9R7 ∙ 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 PPP6R3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP6R3 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			38			38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	0	0

Variants in PPP6R3

This is a list of pathogenic ClinVar variants found in the PPP6R3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-68537797-A-T		not specified	Uncertain significance (Feb 21, 2024)
11-68537848-A-T		not specified	Uncertain significance (Dec 28, 2023)
11-68544850-A-G		not specified	Uncertain significance (Jan 17, 2023)
11-68544947-G-A		not specified	Uncertain significance (Jan 23, 2023)
11-68548109-A-G		not specified	Uncertain significance (Apr 28, 2022)
11-68548136-A-G		not specified	Uncertain significance (Dec 08, 2023)
11-68551183-A-T		not specified	Uncertain significance (Nov 07, 2023)
11-68564311-G-A		not specified	Uncertain significance (Apr 09, 2024)
11-68564316-A-G		not specified	Uncertain significance (Jul 29, 2022)
11-68564365-A-G		not specified	Uncertain significance (Dec 13, 2021)
11-68564409-G-C		not specified	Uncertain significance (Feb 28, 2023)
11-68564427-C-T		not specified	Uncertain significance (Dec 14, 2023)
11-68567047-G-C		not specified	Uncertain significance (Sep 29, 2023)
11-68567138-T-C		not specified	Uncertain significance (Jan 24, 2023)
11-68567148-T-G		not specified	Uncertain significance (Dec 14, 2022)
11-68567153-T-C		not specified	Uncertain significance (Mar 19, 2024)
11-68569751-A-G		not specified	Uncertain significance (Jan 19, 2022)
11-68569812-T-C		not specified	Uncertain significance (Jan 23, 2023)
11-68569848-C-T		not specified	Uncertain significance (Jan 29, 2024)
11-68569859-G-A		not specified	Uncertain significance (Oct 06, 2021)
11-68571040-C-A		not specified	Uncertain significance (Dec 12, 2023)
11-68574110-G-T		not specified	Uncertain significance (Jun 29, 2023)
11-68574120-G-A		not specified	Uncertain significance (Mar 01, 2023)
11-68574170-G-A		not specified	Uncertain significance (Dec 27, 2022)
11-68574201-C-T		not specified	Uncertain significance (Sep 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP6R3	protein_coding	protein_coding	ENST00000393801	23	154617

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.995	0.00513	125734	0	12	125746	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.54	374	468	0.800	0.0000242	5862
Missense in Polyphen		32	98.83	0.32379		1325
Synonymous	-0.185	181	178	1.02	0.0000108	1589
Loss of Function	5.57	8	50.9	0.157	0.00000298	589

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000182	0.000178
Ashkenazi Jewish	0.000219	0.000198
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000355	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000198	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulatory subunit of protein phosphatase 6 (PP6). May function as a scaffolding PP6 subunit. May have an important role in maintaining immune self-tolerance. {ECO:0000269|PubMed:11401438, 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: 0.0966

Intolerance Scores

• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.41

Haploinsufficiency Scores

• pHI: 0.627
• hipred: Y
• hipred_score: 0.601
• ghis: 0.602

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• 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: Ppp6r3

Gene ontology

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