19-40192087-C-T
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002446.4(MAP3K10):c.56C>T(p.Pro19Leu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 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
MAP3K10
NM_002446.4 missense
NM_002446.4 missense
Scores
2
5
11
Clinical Significance
Conservation
PhyloP100: 3.62
Publications
0 publications found
Genes affected
MAP3K10 (HGNC:6849): (mitogen-activated protein kinase kinase kinase 10) The protein encoded by this gene is a member of the serine/threonine kinase family. This kinase has been shown to activate MAPK8/JNK and MKK4/SEK1, and this kinase itself can be phoshorylated, and thus activated by JNK kinases. This kinase functions preferentially on the JNK signaling pathway, and is reported to be involved in nerve growth factor (NGF) induced neuronal apoptosis. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.19174072).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_002446.4. 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 |
|---|---|---|---|---|---|---|---|---|---|
| MAP3K10 | TSL:1 MANE Select | c.56C>T | p.Pro19Leu | missense | Exon 1 of 10 | ENSP00000253055.2 | Q02779 | ||
| MAP3K10 | c.56C>T | p.Pro19Leu | missense | Exon 1 of 10 | ENSP00000527002.1 | ||||
| MAP3K10 | c.56C>T | p.Pro19Leu | missense | Exon 1 of 10 | ENSP00000611253.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.00 AC: 0AN: 131558 AF XY: 0.00
GnomAD2 exomes
AF:
AC:
0
AN:
131558
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1367500Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 672186
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1367500
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
672186
African (AFR)
AF:
AC:
0
AN:
30088
American (AMR)
AF:
AC:
0
AN:
29792
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
21436
East Asian (EAS)
AF:
AC:
0
AN:
36212
South Asian (SAS)
AF:
AC:
0
AN:
72680
European-Finnish (FIN)
AF:
AC:
0
AN:
45436
Middle Eastern (MID)
AF:
AC:
0
AN:
5460
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1069632
Other (OTH)
AF:
AC:
0
AN:
56764
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
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Uncertain
D
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T
M_CAP
Uncertain
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
PhyloP100
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
B
Vest4
MutPred
Gain of catalytic residue at P19 (P = 0.0026)
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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