chrX-18757729-G-T

Variant names:

• chrX-18757729-G-T
• NM_001377996.1:c.499G>T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Moderate BP6_Moderate BS2

The NM_001377996.1(PPEF1):​c.499G>T​(p.Val167Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000147 in 1,086,836 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 23)
  • Exomes 𝑓: 0.000015 (0 hom. 5 hem.)
• Consequence: PPEF1 NM_001377996.1 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.312
• 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: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.18616933).
• BP6: Variant X-18757729-G-T is Benign according to our data. Variant chrX-18757729-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 2528005.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Hemizygotes in GnomAdExome4 at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPEF1	NM_001377996.1	c.499G>T	p.Val167Leu	missense_variant	Exon 5 of 16	ENST00000470157.2	NP_001364925.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPEF1	ENST00000470157.2	c.499G>T	p.Val167Leu	missense_variant	Exon 5 of 16	3	NM_001377996.1	ENSP00000419273.2

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome AF: 0.0000147 AC: 16 AN: 1086836 Hom.: 0 Cov.: 27 AF XY: 0.0000142 AC XY: 5 AN XY: 352464

African (AFR) AF: 0.00 AC: 0 AN: 26178

American (AMR) AF: 0.00 AC: 0 AN: 35156

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19306

East Asian (EAS) AF: 0.00 AC: 0 AN: 30145

South Asian (SAS) AF: 0.00 AC: 0 AN: 53760

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40479

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4104

European-Non Finnish (NFE) AF: 0.0000192 AC: 16 AN: 831976

Other (OTH) AF: 0.00 AC: 0 AN: 45732

GnomAD4 genome Cov.: 23

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Mar 22, 2023

Ambry Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.17	T
BayesDel_noAF	Benign	-0.48
CADD	Benign	0.049
DANN	Benign	0.74
DEOGEN2	Benign	0.19	T;.;T;.
FATHMM_MKL	Benign	0.15	N
LIST_S2	Benign	0.70	T;T;T;T
M_CAP	Benign	0.041	D
MetaRNN	Benign	0.19	T;T;T;T
MetaSVM	Benign	-0.80	T
MutationAssessor	Benign	0.025	N;N;.;.
PhyloP100		0.31
PrimateAI	Benign	0.36	T
PROVEAN	Benign	-0.59	N;N;N;N
REVEL	Benign	0.28
Sift	Benign	0.18	T;T;T;T
Sift4G	Benign	0.10	T;T;T;T
Polyphen		0.0	B;B;.;.
Vest4		0.24
MutPred		0.57		Gain of catalytic residue at V167 (P = 0.0479);Gain of catalytic residue at V167 (P = 0.0479);.;.;
MVP		0.47
MPC		0.48
ClinPred		0.089	T
GERP RS		-7.5
Varity_R		0.10
gMVP		0.59
Mutation Taster		=96/4	polymorphism

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

Other links and lift over

hg19: chrX-18775847;