PPEF1

protein phosphatase with EF-hand domain 1, the group of EF-hand domain containing|Protein phosphatase catalytic subunits

Basic information

Region (hg38): X:18675909-18827921

Previous symbols: [ "PPEF" ]

Links

ENSG00000086717 ∙ NCBI:5475 ∙ OMIM:300109 ∙ HGNC:9243 ∙ Uniprot:O14829 ∙ 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 PPEF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPEF1 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	4
missense			5	2		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	4	2

Variants in PPEF1

This is a list of pathogenic ClinVar variants found in the PPEF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-18733795-T-A		not specified	Uncertain significance (Jan 24, 2024)
X-18749853-C-T			Likely benign (Mar 01, 2023)
X-18757640-A-G		not specified	Uncertain significance (Apr 09, 2024)
X-18757703-A-G		not specified	Uncertain significance (Dec 16, 2023)
X-18757729-G-T		not specified	Likely benign (Mar 22, 2023)
X-18779018-C-T			Benign (Nov 18, 2017)
X-18779035-C-T		not specified	Uncertain significance (Dec 15, 2021)
X-18784036-A-G			Benign (Dec 14, 2017)
X-18789146-C-T		not specified	Uncertain significance (Apr 08, 2022)
X-18803994-A-C		not specified	Uncertain significance (Mar 31, 2024)
X-18806486-T-C			Likely benign (Apr 01, 2022)
X-18806539-G-A		not specified	Likely benign (May 11, 2022)
X-18824064-G-A		not specified	Likely benign (Mar 25, 2024)
X-18827401-A-G		not specified	Uncertain significance (Apr 29, 2024)
X-18827447-A-G		not specified	Uncertain significance (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPEF1	protein_coding	protein_coding	ENST00000361511	16	152011

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.987	0.0127	125564	0	4	125568	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.94	156	241	0.648	0.0000179	4352
Missense in Polyphen		23	83.483	0.27551		1573
Synonymous	0.681	82	90.2	0.909	0.00000720	1159
Loss of Function	4.22	3	26.4	0.114	0.00000214	434

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000135	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000375	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May have a role in the recovery or adaptation response of photoreceptors. May have a role in development.
• Pathway: Signaling by GPCR;Signal Transduction;G alpha (i) signalling events;Inactivation, recovery and regulation of the phototransduction cascade;The phototransduction cascade;Visual phototransduction;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.0975

Intolerance Scores

• loftool: 0.369
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.91

Haploinsufficiency Scores

• pHI: 0.186
• hipred: Y
• hipred_score: 0.654
• ghis: 0.439

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.742

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppef1
• Phenotype: normal phenotype

Gene ontology

• Biological process: protein dephosphorylation;regulation of rhodopsin mediated signaling pathway;detection of stimulus involved in sensory perception
• Cellular component: nucleus;cytosol
• Molecular function: protein serine/threonine phosphatase activity;iron ion binding;calcium ion binding;manganese ion binding