X-18779018-C-A

Variant names:

• chrX-18779018-C-A
• NM_001377996.1:c.567C>A
• PPEF1 p.Leu189Leu

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_001377996.1(PPEF1):​c.567C>A​(p.Leu189Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. L189L) has been classified as Benign.

• Frequency:
  • Genomes: not found (cov: 23)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: PPEF1 NM_001377996.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499
• Publications: 0 publications found

Genes affected

PPEF1 (HGNC:9243): (protein phosphatase with EF-hand domain 1) 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]

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BP7: Synonymous conserved (PhyloP=-0.499 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001377996.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPEF1	NM_001377996.1	MANE Select	c.567C>A	p.Leu189Leu	synonymous	Exon 7 of 16	NP_001364925.1	O14829-1
	PPEF1	NM_001377986.2		c.567C>A	p.Leu189Leu	synonymous	Exon 12 of 21	NP_001364915.1	O14829-1
	PPEF1	NM_001377993.1		c.567C>A	p.Leu189Leu	synonymous	Exon 9 of 18	NP_001364922.1	O14829-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPEF1	ENST00000470157.2	TSL:3 MANE Select	c.567C>A	p.Leu189Leu	synonymous	Exon 7 of 16	ENSP00000419273.2	O14829-1
	PPEF1	ENST00000361511.9	TSL:1	c.567C>A	p.Leu189Leu	synonymous	Exon 13 of 22	ENSP00000354871.3	O14829-1
	PPEF1	ENST00000471570.6	TSL:3	c.567C>A	p.Leu189Leu	synonymous	Exon 8 of 17	ENSP00000509623.1	O14829-1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1083086 Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0 AN XY: 352636

African (AFR) AF: 0.00 AC: 0 AN: 26021

American (AMR) AF: 0.00 AC: 0 AN: 34924

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19169

East Asian (EAS) AF: 0.00 AC: 0 AN: 30111

South Asian (SAS) AF: 0.00 AC: 0 AN: 52993

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40426

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4105

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 829737

Other (OTH) AF: 0.00 AC: 0 AN: 45600

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	3.8
DANN	Benign	0.64
PhyloP100		-0.50

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chrX-18797136;