rs779639376

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_016564.4(CEND1):​c.272C>T​(p.Thr91Ile) variant causes a missense 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. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T91N) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Consequence

CEND1
NM_016564.4 missense

Scores

3
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.53
Variant links:
Genes affected
CEND1 (HGNC:24153): (cell cycle exit and neuronal differentiation 1) The protein encoded by this gene is a neuron-specific protein. The similar protein in pig enhances neuroblastoma cell differentiation in vitro and may be involved in neuronal differentiation in vivo. Multiple pseudogenes have been reported for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.105997115).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CEND1NM_016564.4 linkc.272C>T p.Thr91Ile missense_variant Exon 2 of 2 ENST00000330106.5 NP_057648.2 Q8N111

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CEND1ENST00000330106.5 linkc.272C>T p.Thr91Ile missense_variant Exon 2 of 2 1 NM_016564.4 ENSP00000328336.4 Q8N111
CEND1ENST00000524587.1 linkn.345C>T non_coding_transcript_exon_variant Exon 2 of 2 3

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.16
BayesDel_addAF
Benign
-0.25
T
BayesDel_noAF
Benign
-0.60
CADD
Benign
18
DANN
Uncertain
0.99
DEOGEN2
Benign
0.38
T
Eigen
Benign
-0.85
Eigen_PC
Benign
-0.86
FATHMM_MKL
Benign
0.098
N
LIST_S2
Benign
0.41
T
M_CAP
Benign
0.013
T
MetaRNN
Benign
0.11
T
MetaSVM
Benign
-0.97
T
MutationAssessor
Benign
1.3
L
PrimateAI
Uncertain
0.66
T
PROVEAN
Uncertain
-2.4
N
REVEL
Benign
0.061
Sift
Benign
0.056
T
Sift4G
Benign
0.085
T
Polyphen
0.28
B
Vest4
0.032
MutPred
0.21
Loss of glycosylation at T91 (P = 7e-04);
MVP
0.043
MPC
0.60
ClinPred
0.25
T
GERP RS
2.6
Varity_R
0.050
gMVP
0.13

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-788305; API