1-12022869-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000235332.6(MIIP):​c.499A>T​(p.Lys167Ter) variant causes a stop gained change involving the alteration of a non-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: 30)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

MIIP
ENST00000235332.6 stop_gained

Scores

2
1
4

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.41
Variant links:
Genes affected
MIIP (HGNC:25715): (migration and invasion inhibitory protein) This gene encodes a protein that interacts with the oncogene protein insulin-like growth factor binding protein 2 and may function as an inhibitor of cell migration and invasion. This protein also interacts with the cell division protein 20 and may be involved in regulating mitotic progression. This protein may function as a tumor suppressor by inhibiting the growth or certain cancers. [provided by RefSeq, Sep 2011]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MIIPNM_021933.4 linkuse as main transcriptc.499A>T p.Lys167Ter stop_gained 4/10 ENST00000235332.6 NP_068752.2
MIIPXM_011541895.2 linkuse as main transcriptc.499A>T p.Lys167Ter stop_gained 4/10 XP_011540197.1
MIIPXM_011541896.2 linkuse as main transcriptc.499A>T p.Lys167Ter stop_gained 4/10 XP_011540198.1
MIIPXM_005263487.5 linkuse as main transcriptc.499A>T p.Lys167Ter stop_gained 4/10 XP_005263544.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MIIPENST00000235332.6 linkuse as main transcriptc.499A>T p.Lys167Ter stop_gained 4/101 NM_021933.4 ENSP00000235332 P1Q5JXC2-1
MIIPENST00000466860.5 linkuse as main transcriptn.258A>T non_coding_transcript_exon_variant 2/65
MIIPENST00000478749.5 linkuse as main transcriptn.472A>T non_coding_transcript_exon_variant 3/62
MIIPENST00000498685.5 linkuse as main transcriptn.6A>T non_coding_transcript_exon_variant 1/62

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1456766
Hom.:
0
Cov.:
46
AF XY:
0.00
AC XY:
0
AN XY:
724226
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:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.36
D
BayesDel_noAF
Pathogenic
0.28
CADD
Pathogenic
37
DANN
Uncertain
0.99
Eigen
Benign
0.024
Eigen_PC
Benign
-0.30
FATHMM_MKL
Benign
0.16
N
MutationTaster
Benign
4.1e-11
P;P
Vest4
0.066
GERP RS
1.5
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.070
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: rs2295283; hg19: chr1-12082926; API