rs767528335

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_173468.4(MOB1B):​c.302C>A​(p.Thr101Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000687 in 1,455,950 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. T101M) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

MOB1B
NM_173468.4 missense

Scores

2
5
12

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.80
Variant links:
Genes affected
MOB1B (HGNC:29801): (MOB kinase activator 1B) 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. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.27973217).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MOB1BNM_173468.4 linkc.302C>A p.Thr101Lys missense_variant Exon 4 of 6 ENST00000309395.7 NP_775739.1 Q7L9L4-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MOB1BENST00000309395.7 linkc.302C>A p.Thr101Lys missense_variant Exon 4 of 6 1 NM_173468.4 ENSP00000310189.3 Q7L9L4-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000406
AC:
1
AN:
246146
Hom.:
0
AF XY:
0.00000752
AC XY:
1
AN XY:
132998
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000344
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
6.87e-7
AC:
1
AN:
1455950
Hom.:
0
Cov.:
29
AF XY:
0.00000138
AC XY:
1
AN XY:
724186
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000118
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.35
BayesDel_addAF
Uncertain
0.13
D
BayesDel_noAF
Uncertain
0.060
CADD
Uncertain
23
DANN
Benign
0.86
DEOGEN2
Benign
0.036
.;T;.
Eigen
Benign
-0.18
Eigen_PC
Benign
0.12
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.96
D;D;D
M_CAP
Benign
0.025
T
MetaRNN
Benign
0.28
T;T;T
MetaSVM
Benign
-0.96
T
MutationAssessor
Benign
0.24
.;N;.
PrimateAI
Pathogenic
0.91
D
PROVEAN
Benign
-0.85
N;N;N
REVEL
Uncertain
0.35
Sift
Benign
0.90
T;T;T
Sift4G
Benign
0.93
T;T;T
Polyphen
0.0010
.;B;.
Vest4
0.69, 0.69
MutPred
0.40
.;Gain of methylation at T101 (P = 0.0124);.;
MVP
0.74
MPC
0.14
ClinPred
0.39
T
GERP RS
6.0
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
2.7
Varity_R
0.18
gMVP
0.59

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

LitVar

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

Other links and lift over

dbSNP: rs767528335; hg19: chr4-71840896; API