PPP4R3A

protein phosphatase 4 regulatory subunit 3A, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 14:91457508-91510554

Previous symbols: [ "KIAA2010", "SMEK1" ]

Links

ENSG00000100796 ∙ NCBI:55671 ∙ OMIM:610351 ∙ HGNC:20219 ∙ Uniprot:Q6IN85 ∙ 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 PPP4R3A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP4R3A 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					1	1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	1

Variants in PPP4R3A

This is a list of pathogenic ClinVar variants found in the PPP4R3A region.

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

Position	Type	Phenotype	Significance	ClinVar
14-91475932-G-A		not specified	Benign (May 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP4R3A	protein_coding	protein_coding	ENST00000554684	15	52944

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000825	125719	0	4	125723	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.64	215	427	0.504	0.0000216	5413
Missense in Polyphen		86	217.5	0.39541		2815
Synonymous	-1.44	177	154	1.15	0.00000780	1520
Loss of Function	5.41	3	39.9	0.0752	0.00000215	505

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000116	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000116	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulatory subunit of serine/threonine-protein phosphatase 4. May regulate the activity of PPP4C at centrosomal microtubule organizing centers. The PPP4C-PPP4R2-PPP4R3A PP4 complex specifically dephosphorylates H2AFX phosphorylated on 'Ser-140' (gamma-H2AFX) generated during DNA replication and required for DNA DSB repair. {ECO:0000269|PubMed:18614045}.
• Pathway: Glucagon signaling pathway - Homo sapiens (human);IGF-Ncore;Integrated Breast Cancer Pathway (Consensus)

Intolerance Scores

• rvis_EVS: -0.65
• rvis_percentile_EVS: 16.36

Haploinsufficiency Scores

• pHI: 0.843
• hipred: Y
• hipred_score: 0.717
• ghis: 0.659

Mouse Genome Informatics

• Gene name: Ppp4r3a

Gene ontology

• Cellular component: nucleoplasm;cytoplasm;microtubule organizing center