chr11-108158947-C-T
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_002519.3(NPAT):c.4279G>A(p.Glu1427Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
NPAT
NM_002519.3 missense
NM_002519.3 missense
Scores
6
7
5
Clinical Significance
Conservation
PhyloP100: 7.27
Publications
0 publications found
Genes affected
NPAT (HGNC:7896): (nuclear protein, coactivator of histone transcription) Enables protein C-terminus binding activity; transcription coactivator activity; and transcription corepressor activity. Involved in positive regulation of transcription by RNA polymerase II and regulation of transcription involved in G1/S transition of mitotic cell cycle. Located in Cajal body; Gemini of coiled bodies; and cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
NPAT Gene-Disease associations (from GenCC):
- colorectal cancerInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_002519.3. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| NPAT | TSL:1 MANE Select | c.4279G>A | p.Glu1427Lys | missense | Exon 18 of 18 | ENSP00000278612.8 | Q14207 | ||
| NPAT | c.4306G>A | p.Glu1436Lys | missense | Exon 18 of 18 | ENSP00000605849.1 | ||||
| NPAT | c.4279G>A | p.Glu1427Lys | missense | Exon 18 of 18 | ENSP00000520908.1 | Q14207 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1431674Hom.: 0 Cov.: 26 AF XY: 0.00 AC XY: 0AN XY: 714094
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1431674
Hom.:
Cov.:
26
AF XY:
AC XY:
0
AN XY:
714094
African (AFR)
AF:
AC:
0
AN:
32936
American (AMR)
AF:
AC:
0
AN:
44654
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25892
East Asian (EAS)
AF:
AC:
0
AN:
39398
South Asian (SAS)
AF:
AC:
0
AN:
85670
European-Finnish (FIN)
AF:
AC:
0
AN:
51168
Middle Eastern (MID)
AF:
AC:
0
AN:
5694
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1086850
Other (OTH)
AF:
AC:
0
AN:
59412
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Benign
D
MetaRNN
Uncertain
D
MetaSVM
Benign
T
MutationAssessor
Benign
L
PhyloP100
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D
REVEL
Uncertain
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MutPred
Gain of ubiquitination at E1427 (P = 0.0109)
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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