rs17850615

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate

The NM_002861.5(PCYT2):​c.730T>C​(p.Tyr244His) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)

Consequence

PCYT2
NM_002861.5 missense

Scores

12
6
1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.80
Variant links:
Genes affected
PCYT2 (HGNC:8756): (phosphate cytidylyltransferase 2, ethanolamine) This gene encodes an enzyme that catalyzes the formation of CDP-ethanolamine from CTP and phosphoethanolamine in the Kennedy pathway of phospholipid synthesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.911

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PCYT2NM_002861.5 linkuse as main transcriptc.730T>C p.Tyr244His missense_variant 8/13 ENST00000538936.7 NP_002852.1 Q99447-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PCYT2ENST00000538936.7 linkuse as main transcriptc.730T>C p.Tyr244His missense_variant 8/131 NM_002861.5 ENSP00000439245.3 Q99447-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.70
BayesDel_addAF
Pathogenic
0.54
D
BayesDel_noAF
Pathogenic
0.53
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Pathogenic
0.82
D;.;.;.;.;.;D;D
Eigen
Uncertain
0.58
Eigen_PC
Uncertain
0.50
FATHMM_MKL
Uncertain
0.86
D
LIST_S2
Pathogenic
0.98
D;.;D;D;D;D;D;D
M_CAP
Pathogenic
0.52
D
MetaRNN
Pathogenic
0.91
D;D;D;D;D;D;D;D
MetaSVM
Pathogenic
1.0
D
MutationAssessor
Uncertain
2.4
M;.;.;.;.;.;.;.
PrimateAI
Uncertain
0.66
T
PROVEAN
Pathogenic
-4.6
D;D;D;.;.;.;.;.
REVEL
Pathogenic
0.90
Sift
Pathogenic
0.0
D;D;D;.;.;.;.;.
Sift4G
Pathogenic
0.0
D;D;D;D;D;D;.;D
Polyphen
1.0
D;.;.;.;.;.;.;.
Vest4
0.94
MutPred
0.64
Gain of catalytic residue at R242 (P = 0.0833);.;.;Gain of catalytic residue at R242 (P = 0.0833);.;.;.;.;
MVP
0.94
MPC
1.9
ClinPred
1.0
D
GERP RS
4.8
Varity_R
0.88
gMVP
0.84

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs17850615; hg19: chr17-79864369; API