5-62487831-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_016338.5(IPO11):c.1279G>T(p.Val427Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000522 in 1,609,902 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000055 ( 0 hom. )
Consequence
IPO11
NM_016338.5 missense
NM_016338.5 missense
Scores
8
11
Clinical Significance
Conservation
PhyloP100: 6.88
Genes affected
IPO11 (HGNC:20628): (importin 11) Importins, including IPO11, are a members of the karyopherin/importin-beta family of transport receptors (see KPNB1; 602738) that mediate nucleocytoplasmic transport of protein and RNA cargoes (Plafker and Macara, 2000 [PubMed 11032817]).[supplied by OMIM, Sep 2008]
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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 | UniProt |
---|---|---|---|---|---|---|---|
IPO11 | NM_016338.5 | c.1279G>T | p.Val427Leu | missense_variant | 13/30 | ENST00000325324.11 | |
IPO11 | NM_001134779.2 | c.1399G>T | p.Val467Leu | missense_variant | 13/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IPO11 | ENST00000325324.11 | c.1279G>T | p.Val427Leu | missense_variant | 13/30 | 1 | NM_016338.5 | P1 | |
IPO11 | ENST00000409296.7 | c.1399G>T | p.Val467Leu | missense_variant | 13/30 | 2 | |||
IPO11 | ENST00000424533.5 | c.1279G>T | p.Val427Leu | missense_variant, NMD_transcript_variant | 13/29 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152000Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000124 AC: 31AN: 248996Hom.: 0 AF XY: 0.000134 AC XY: 18AN XY: 134752
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GnomAD4 exome AF: 0.0000549 AC: 80AN: 1457784Hom.: 0 Cov.: 30 AF XY: 0.0000717 AC XY: 52AN XY: 725006
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GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152118Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74350
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 13, 2023 | The c.1399G>T (p.V467L) alteration is located in exon 13 (coding exon 13) of the IPO11 gene. This alteration results from a G to T substitution at nucleotide position 1399, causing the valine (V) at amino acid position 467 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
D;T
Sift4G
Benign
T;T
Polyphen
P;P
Vest4
MutPred
Loss of catalytic residue at V427 (P = 0.0139);.;
MVP
MPC
0.21
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: 10
Find out detailed SpliceAI scores and Pangolin per-transcript scores at