rs1554676260
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000438773.4(TRAPPC9):c.1294C>A(p.Leu432Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. L432L) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 33)
Consequence
TRAPPC9
ENST00000438773.4 missense
ENST00000438773.4 missense
Scores
2
9
8
Clinical Significance
Conservation
PhyloP100: 7.62
Genes affected
TRAPPC9 (HGNC:30832): (trafficking protein particle complex subunit 9) This gene encodes a protein that likely plays a role in NF-kappa-B signaling. Mutations in this gene have been associated with autosomal-recessive cognitive disability. Alternatively spliced transcript variants have been described.[provided by RefSeq, Feb 2010]
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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 |
---|---|---|---|---|---|---|---|---|
TRAPPC9 | NM_001160372.4 | c.1294C>A | p.Leu432Ile | missense_variant | 8/23 | ENST00000438773.4 | NP_001153844.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRAPPC9 | ENST00000438773.4 | c.1294C>A | p.Leu432Ile | missense_variant | 8/23 | 1 | NM_001160372.4 | ENSP00000405060 | P1 | |
TRAPPC9 | ENST00000520857.5 | c.826C>A | p.Leu276Ile | missense_variant | 6/21 | 1 | ENSP00000430116 | |||
TRAPPC9 | ENST00000648948.2 | c.1294C>A | p.Leu432Ile | missense_variant | 8/23 | ENSP00000498020 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
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 | Genetic Services Laboratory, University of Chicago | Apr 14, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;T;.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
.;.;D;D
M_CAP
Benign
T
MetaRNN
Uncertain
D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;.;L
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
.;N;N;.
REVEL
Benign
Sift
Benign
.;T;T;.
Sift4G
Uncertain
.;D;D;.
Polyphen
P;P;P;P
Vest4
0.60, 0.61
MutPred
Gain of methylation at K430 (P = 0.0688);Gain of methylation at K430 (P = 0.0688);.;Gain of methylation at K430 (P = 0.0688);
MVP
0.30
MPC
1.3
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