X-18779016-CTC-TTA

Variant names:

• chrX-18779016-CTC-TTA
• NM_001377996.1:c.565_567delCTCinsTTA
• PPEF1 p.190

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001377996.1(PPEF1):​c.565_567delCTCinsTTA​(p.190) variant causes a synonymous change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. 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: 22)
• Consequence: PPEF1 NM_001377996.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.96
• 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: Uncertain_significance. The variant received 0 ACMG points.

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.565_567delCTCinsTTA	p.190	synonymous	N/A	NP_001364925.1	O14829-1
	PPEF1	NM_001377986.2		c.565_567delCTCinsTTA	p.190	synonymous	N/A	NP_001364915.1	O14829-1
	PPEF1	NM_001377993.1		c.565_567delCTCinsTTA	p.190	synonymous	N/A	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.565_567delCTCinsTTA	p.190	synonymous	N/A	ENSP00000419273.2	O14829-1
	PPEF1	ENST00000361511.9	TSL:1	c.565_567delCTCinsTTA	p.190	synonymous	N/A	ENSP00000354871.3	O14829-1
	PPEF1	ENST00000471570.6	TSL:3	c.565_567delCTCinsTTA	p.190	synonymous	N/A	ENSP00000509623.1	O14829-1

Frequencies

GnomAD3 genomes Cov.: 22

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		6.0

Splicing

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-18797134;