rs121434395
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1PM2PP3_ModeratePP5_Moderate
The NM_004621.6(TRPC6):c.2689G>A(p.Glu897Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Genomes: not found (cov: 33)
Consequence
TRPC6
NM_004621.6 missense
NM_004621.6 missense
Scores
13
5
1
Clinical Significance
Conservation
PhyloP100: 7.71
Genes affected
TRPC6 (HGNC:12338): (transient receptor potential cation channel subfamily C member 6) The protein encoded by this gene forms a receptor-activated calcium channel in the cell membrane. The channel is activated by diacylglycerol and is thought to be under the control of a phosphatidylinositol second messenger system. Activation of this channel occurs independently of protein kinase C and is not triggered by low levels of intracellular calcium. Defects in this gene are a cause of focal segmental glomerulosclerosis 2 (FSGS2). [provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
PM1
?
In a helix (size 36) in uniprot entity TRPC6_HUMAN there are 6 pathogenic changes around while only 0 benign (100%) in NM_004621.6
PM2
?
Very rare variant in population databases, with high coverage;
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.894
PP5
?
Variant 11-101453062-C-T is Pathogenic according to our data. Variant chr11-101453062-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 6156.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRPC6 | NM_004621.6 | c.2689G>A | p.Glu897Lys | missense_variant | 13/13 | ENST00000344327.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPC6 | ENST00000344327.8 | c.2689G>A | p.Glu897Lys | missense_variant | 13/13 | 1 | NM_004621.6 | P1 | |
TRPC6 | ENST00000360497.4 | c.2524G>A | p.Glu842Lys | missense_variant | 12/12 | 1 | |||
TRPC6 | ENST00000348423.8 | c.2341G>A | p.Glu781Lys | missense_variant | 11/11 | 1 | |||
TRPC6 | ENST00000532133.5 | c.2455G>A | p.Glu819Lys | missense_variant | 12/12 | 5 |
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
Alfa
AF:
Hom.:
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:3
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Inborn genetic diseases Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 21, 2023 | The c.2689G>A (p.E897K) alteration is located in exon 13 (coding exon 13) of the TRPC6 gene. This alteration results from a G to A substitution at nucleotide position 2689, causing the glutamic acid (E) at amino acid position 897 to be replaced by a lysine (K). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This variant has been identified in multiple individuals with clinical features consistent with TRPC6-related focal segmental glomerulosclerosis (Reiser, 2005; Groopman, 2019; Lu, 2022). This amino acid position is highly conserved in available vertebrate species. Based on internal structural analysis, E897K is more disruptive to the CH2 domain of TRPC6 than our internal threshold for deleterious destabilization, though there are no comparable internally pathogenic variants nearby for comparison (Tang, 2018; Guo, 2022). Functional studies show that E897K leads to altered protein function (Reiser, 2005; Riehle, 2016; Polat, 2019; Schlöndorff, 2009). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as likely pathogenic. - |
not provided Pathogenic:1
Pathogenic, no assertion criteria provided | research | Gharavi Laboratory, Columbia University | Sep 16, 2018 | - - |
Focal segmental glomerulosclerosis 2 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 01, 2005 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Pathogenic
DEOGEN2
Pathogenic
D;.;.;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D;D;D;D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D;D
MetaSVM
Uncertain
D
MutationAssessor
Pathogenic
M;.;.;.
MutationTaster
Benign
A;A;A;A
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D;D;D;D
REVEL
Pathogenic
Sift
Uncertain
D;D;D;D
Sift4G
Uncertain
D;D;D;D
Polyphen
D;.;D;.
Vest4
MutPred
Gain of ubiquitination at E897 (P = 0.0101);.;.;.;
MVP
MPC
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