GeneBe

rs1363126357

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_201403.3(MOB3C):​c.376G>T​(p.Glu126*) variant causes a stop gained change involving the alteration of a conserved nucleotide. 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. Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

MOB3C
NM_201403.3 stop_gained

Scores

4
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.89

Publications

1 publications found
Variant links:
Genes affected
MOB3C (HGNC:29800): (MOB kinase activator 3C) The protein encoded by this gene is similar to the yeast Mob1 protein. Yeast Mob1 binds Mps1p, a protein kinase essential for spindle pole body duplication and mitotic checkpoint regulation. Alternatively spliced transcript variants encoding distinct isoforms have been observed. [provided by RefSeq, Jul 2008]
MKNK1 (HGNC:7110): (MAPK interacting serine/threonine kinase 1) This gene encodes a Ser/Thr protein kinase that interacts with, and is activated by ERK1 and p38 mitogen-activated protein kinases, and thus may play a role in the response to environmental stress and cytokines. This kinase may also regulate transcription by phosphorylating eIF4E via interaction with the C-terminal region of eIF4G. Alternatively spliced transcript variants have been noted for this gene. [provided by RefSeq, Jan 2012]

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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_201403.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
MOB3C
NM_201403.3
MANE Select
c.376G>Tp.Glu126*
stop_gained
Exon 2 of 4NP_958805.1Q70IA8
MOB3C
NM_145279.5
c.376G>Tp.Glu126*
stop_gained
Exon 2 of 4NP_660322.3

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
MOB3C
ENST00000319928.9
TSL:2 MANE Select
c.376G>Tp.Glu126*
stop_gained
Exon 2 of 4ENSP00000315113.3Q70IA8
MOB3C
ENST00000271139.13
TSL:1
c.376G>Tp.Glu126*
stop_gained
Exon 2 of 4ENSP00000271139.9Q70IA8
MOB3C
ENST00000371940.1
TSL:1
c.376G>Tp.Glu126*
stop_gained
Exon 1 of 3ENSP00000361008.2Q70IA8

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1425814
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
704348
African (AFR)
AF:
0.00
AC:
0
AN:
32608
American (AMR)
AF:
0.00
AC:
0
AN:
41450
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
23826
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39206
South Asian (SAS)
AF:
0.00
AC:
0
AN:
81714
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
52152
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5598
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1090590
Other (OTH)
AF:
0.00
AC:
0
AN:
58670
GnomAD4 genome
Cov.:
33
Alfa
AF:
0.00
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.57
D
BayesDel_noAF
Pathogenic
0.58
CADD
Pathogenic
39
DANN
Uncertain
1.0
Eigen
Pathogenic
1.1
Eigen_PC
Pathogenic
1.0
FATHMM_MKL
Uncertain
0.94
D
PhyloP100
7.9
Vest4
0.31
GERP RS
5.3
Mutation Taster
=3/197
disease causing (fs/PTC)

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

Other links and lift over

dbSNP: rs1363126357; hg19: chr1-47078618; API