PPEF1

protein-coding

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

Gene summary

This gene encodes a member of the serine/threonine protein phosphatase with EF-hand motif family. The protein contains a protein phosphatase catalytic domain, and at least two EF-hand calcium-binding motifs in its C terminus. Although its substrate(s) is unknown, the encoded protein has been suggested to play a role in specific sensory neuron function and/or development. This gene shares high sequence similarity with the Drosophila retinal degeneration C (rdgC) gene. Several alternatively spliced transcript variants, each encoding a distinct isoform, have been described. [provided by RefSeq, Jul 2008]

Previous symbols:

PPEF

MANE transcript

NM_001377996.1

Inheritance

—

ClinVar variants

U:130B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chrX:18,675,909-18,827,921

External References & Databases

Ensembl (ENSG00000086717)

Transcript & Mutation Effects

hg38 • Region Span ~152.0 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PPEF1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 30

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001377996.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			18 clinvar	2 clinvar	2 clinvar	22
missense			87 clinvar	6 clinvar		93
nonsense			9 clinvar			9
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			16 clinvar			16
Total	0	0	130	8	2	140

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 40 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001377996.1	RefSeq	NP_001364925.1	16	MANE Select
ENST00000470157.2	Ensembl	ENSP00000419273.2	16	MANE Select
NM_001377986.2	RefSeq	NP_001364915.1	16	Standard
NM_001377993.1	RefSeq	NP_001364922.1	16	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signaling by GPCR
Signal Transduction
G alpha (i) signalling events
Inactivation, recovery and regulation of the phototransduction cascade
The phototransduction cascade

Biological Process

protein dephosphorylation
regulation of rhodopsin mediated signaling pathway
detection of stimulus involved in sensory perception

Molecular Function

protein serine/threonine phosphatase activity
iron ion binding
calcium ion binding
manganese ion binding

Cellular Component

nucleus
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000361511
Coding exons: 16
Length: 152011
Individuals with no LoFs: 125564
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125568
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.94	156	241	0.648	0.0000179	4352
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00014	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000038	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May have a role in the recovery or adaptation response of photoreceptors. May have a role in development.;

Recessive Scores

pRec: 0.0975

Intolerance Scores

LoFtool: 0.369
RVIS EVS: -0.16
RVIS percentile EVS: 41.91

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.742

Gene Damage Prediction

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