PPEF2

protein phosphatase with EF-hand domain 2, the group of EF-hand domain containing|Protein phosphatase catalytic subunits

Basic information

Region (hg38): 4:75859864-75902571

Links

ENSG00000156194 ∙ NCBI:5470 ∙ OMIM:602256 ∙ HGNC:9244 ∙ Uniprot:O14830 ∙ 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 PPEF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPEF2 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				2		2
missense			45	1		46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	3	0

Variants in PPEF2

This is a list of pathogenic ClinVar variants found in the PPEF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-75860692-C-G		not specified	Uncertain significance (Sep 01, 2021)
4-75860765-G-A		not specified	Uncertain significance (May 04, 2022)
4-75860770-G-T		not specified	Uncertain significance (Apr 20, 2024)
4-75860785-T-C		not specified	Uncertain significance (Nov 29, 2023)
4-75860839-A-C		not specified	Uncertain significance (Jul 21, 2021)
4-75860903-C-T		not specified	Uncertain significance (Jun 21, 2021)
4-75864473-T-A		not specified	Uncertain significance (Oct 06, 2021)
4-75866208-T-A		not specified	Uncertain significance (Nov 30, 2021)
4-75866216-G-C		not specified	Uncertain significance (Jun 24, 2022)
4-75866245-T-A		not specified	Uncertain significance (Jul 13, 2022)
4-75867331-G-A		not specified	Uncertain significance (Jul 12, 2022)
4-75867364-G-A		not specified	Uncertain significance (May 25, 2022)
4-75867388-C-T		not specified	Uncertain significance (May 11, 2022)
4-75867398-C-T			Likely benign (May 01, 2022)
4-75872031-C-T		not specified	Uncertain significance (Aug 21, 2023)
4-75872043-G-T		not specified	Uncertain significance (Jul 25, 2023)
4-75872074-C-T		not specified	Uncertain significance (Sep 27, 2022)
4-75872079-T-C		not specified	Uncertain significance (Jan 22, 2024)
4-75872157-A-G		not specified	Uncertain significance (Feb 27, 2023)
4-75873263-G-C		not specified	Uncertain significance (Feb 16, 2023)
4-75873288-G-C		not specified	Uncertain significance (Mar 16, 2024)
4-75876294-C-A		not specified	Uncertain significance (Mar 07, 2024)
4-75876325-C-T		not specified	Uncertain significance (Feb 13, 2023)
4-75876326-G-A			Likely benign (May 01, 2022)
4-75876371-C-G		not specified	Uncertain significance (Jan 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPEF2	protein_coding	protein_coding	ENST00000286719	16	42705

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.37e-15	0.652	117862	140	7746	125748	0.0319

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0442	434	437	0.994	0.0000251	4950
Missense in Polyphen		162	164.57	0.98441		1998
Synonymous	-0.683	176	165	1.07	0.00000926	1416
Loss of Function	1.73	28	39.8	0.704	0.00000207	450

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0953	0.0953
Ashkenazi Jewish	0.0431	0.0390
East Asian	0.00355	0.00310
Finnish	0.0318	0.0312
European (Non-Finnish)	0.0407	0.0386
Middle Eastern	0.00355	0.00310
South Asian	0.0131	0.0111
Other	0.0371	0.0333

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in phototransduction. May dephosphorylate photoactivated rhodopsin. May function as a calcium sensing regulator of ionic currents, energy production or synaptic transmission.

Recessive Scores

• pRec: 0.0896

Intolerance Scores

• loftool: 0.831
• rvis_EVS: 1.16
• rvis_percentile_EVS: 92.66

Haploinsufficiency Scores

• pHI: 0.379
• hipred: N
• hipred_score: 0.196

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.794

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppef2
• Phenotype: normal phenotype

Gene ontology

• Biological process: protein dephosphorylation;visual perception;negative regulation of peptidyl-threonine phosphorylation;regulation of MAP kinase activity;negative regulation of MAPK cascade;regulation of JUN kinase activity;detection of stimulus involved in sensory perception
• Cellular component: photoreceptor outer segment;photoreceptor inner segment;nucleus;cytosol
• Molecular function: protein serine/threonine phosphatase activity;iron ion binding;calcium ion binding;manganese ion binding;Hsp70 protein binding;mitogen-activated protein kinase kinase kinase binding;Hsp90 protein binding