PPP4R4

protein phosphatase 4 regulatory subunit 4, the group of Armadillo like helical domain containing|Protein phosphatase 4 regulatory subunits|Cilia and flagella associated

Basic information

Region (hg38): 14:94146128-94279734

Previous symbols: [ "KIAA1622" ]

Links

ENSG00000119698 ∙ NCBI:57718 ∙ OMIM:616790 ∙ HGNC:23788 ∙ Uniprot:Q6NUP7 ∙ 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 PPP4R4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP4R4 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			34			34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	0	0

Variants in PPP4R4

This is a list of pathogenic ClinVar variants found in the PPP4R4 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-94174485-C-T		not specified	Uncertain significance (Sep 26, 2024)
14-94174502-A-G		not specified	Uncertain significance (Mar 24, 2023)
14-94174520-G-C		not specified	Uncertain significance (Apr 18, 2023)
14-94174550-A-G		not specified	Uncertain significance (Nov 30, 2021)
14-94174560-G-C		not specified	Uncertain significance (Sep 21, 2023)
14-94174568-C-G		not specified	Uncertain significance (Nov 14, 2024)
14-94176121-T-C		not specified	Uncertain significance (Nov 10, 2024)
14-94230624-C-T		not specified	Uncertain significance (Aug 19, 2024)
14-94230680-T-C		not specified	Uncertain significance (Jan 17, 2024)
14-94231308-G-A		not specified	Uncertain significance (Apr 07, 2022)
14-94233702-C-A		not specified	Uncertain significance (Apr 25, 2023)
14-94233749-G-C		not specified	Uncertain significance (Nov 14, 2023)
14-94233756-A-T		not specified	Uncertain significance (Mar 31, 2023)
14-94234639-G-A		not specified	Uncertain significance (May 11, 2022)
14-94237576-C-G		not specified	Uncertain significance (Oct 12, 2024)
14-94237579-A-G		not specified	Uncertain significance (Dec 08, 2023)
14-94241828-T-A		not specified	Uncertain significance (Oct 03, 2022)
14-94241897-A-T		not specified	Uncertain significance (Oct 09, 2024)
14-94241905-A-T		not specified	Uncertain significance (Jul 07, 2024)
14-94241956-C-T		not specified	Uncertain significance (Nov 14, 2024)
14-94242296-T-C		not specified	Uncertain significance (Dec 15, 2022)
14-94242307-G-A		not specified	Uncertain significance (Apr 04, 2024)
14-94242331-C-T		not specified	Uncertain significance (Jan 31, 2022)
14-94242373-C-G		not specified	Uncertain significance (Nov 06, 2023)
14-94245602-A-G		not specified	Uncertain significance (Mar 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP4R4	protein_coding	protein_coding	ENST00000304338	25	133608

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.25e-9	1.00	125709	1	38	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	384	454	0.847	0.0000232	5696
Missense in Polyphen		83	119.03	0.69729		1517
Synonymous	0.721	148	160	0.927	0.00000778	1628
Loss of Function	3.80	24	54.1	0.443	0.00000318	657

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000217	0.000216
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.000164	0.000163
Finnish	0.000232	0.000231
European (Non-Finnish)	0.000161	0.000158
Middle Eastern	0.000164	0.000163
South Asian	0.000239	0.000196
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative regulatory subunit of serine/threonine-protein phosphatase 4.

Recessive Scores

• pRec: 0.0888

Intolerance Scores

• loftool: 0.148
• rvis_EVS: -1.09
• rvis_percentile_EVS: 7.15

Haploinsufficiency Scores

• pHI: 0.106
• hipred: Y
• hipred_score: 0.578
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.755

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp4r4

Gene ontology

• Biological process: blastocyst hatching;negative regulation of phosphoprotein phosphatase activity;regulation of protein serine/threonine phosphatase activity
• Cellular component: cytoplasm;cytosol;protein serine/threonine phosphatase complex
• Molecular function: protein binding;protein phosphatase regulator activity