rs771464310
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001395513.1(TMPRSS9):c.3142G>A(p.Ala1048Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 33)
Consequence
TMPRSS9
NM_001395513.1 missense
NM_001395513.1 missense
Scores
13
6
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.12
Genes affected
TMPRSS9 (HGNC:30079): (transmembrane serine protease 9) The protein encoded by this gene is a membrane-bound type II serine polyprotease that is cleaved to release three different proteases. Two of the proteases are active and can be inhibited by serine protease inhibitors, and one is thought to be catalytically inactive. This gene enhances the invasive capability of pancreatic cancer cells and may be involved in cancer progression. [provided by RefSeq, Jul 2016]
TIMM13 (HGNC:11816): (translocase of inner mitochondrial membrane 13) This gene encodes a member of the evolutionarily conserved TIMM (translocase of inner mitochondrial membrane) family of proteins that function as chaperones in the import of proteins from the cytoplasm into the mitochondrial inner membrane. Proteins of this family play a role in collecting substrate proteins from the translocase of the outer mitochondrial membrane (TOM) complex and delivering them to either the sorting and assembly machinery in the outer mitochondrial membrane (SAM) complex or the TIMM22 complex in the inner mitochondrial membrane. The encoded protein and the translocase of mitochondrial inner membrane 8a protein form a 70 kDa complex in the intermembrane space. [provided by RefSeq, Jul 2013]
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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
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| TMPRSS9 | ENST00000696167.1 | c.3142G>A | p.Ala1048Thr | missense_variant | Exon 19 of 19 | NM_001395513.1 | ENSP00000512457.1 | |||
| TIMM13 | ENST00000215570 | c.*1000C>T | 3_prime_UTR_variant | Exon 3 of 3 | 1 | NM_012458.4 | ENSP00000215570.2 | |||
| TMPRSS9 | ENST00000648592.1 | c.3142G>A | p.Ala1048Thr | missense_variant | Exon 18 of 18 | ENSP00000498031.1 | ||||
| TMPRSS9 | ENST00000649857.1 | c.3040G>A | p.Ala1014Thr | missense_variant | Exon 18 of 18 | ENSP00000497651.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
.;T;T
M_CAP
Uncertain
D
MetaRNN
Uncertain
D;D;D
MetaSVM
Uncertain
D
MutationAssessor
Benign
N;.;N
PrimateAI
Uncertain
T
PROVEAN
Uncertain
.;.;D
REVEL
Uncertain
Sift
Uncertain
.;.;D
Sift4G
Benign
.;.;T
Polyphen
D;.;D
Vest4
0.60
MutPred
Gain of phosphorylation at A1014 (P = 0.0461);.;Gain of phosphorylation at A1014 (P = 0.0461);
MVP
0.83
MPC
0.43
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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
Publications
No publications associated with this variant yet.