X-111776462-A-G
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_012471.3(TRPC5):c.2773T>C(p.Ser925Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000911 in 1,097,671 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Genomes: not found (cov: 22)
Exomes 𝑓: 9.1e-7 ( 0 hom. 1 hem. )
Consequence
TRPC5
NM_012471.3 missense
NM_012471.3 missense
Scores
3
8
5
Clinical Significance
Conservation
PhyloP100: 8.24
Publications
0 publications found
Genes affected
TRPC5 (HGNC:12337): (transient receptor potential cation channel subfamily C member 5) This gene belongs to the transient receptor family. It encodes one of the seven mammalian TRPC (transient receptor potential channel) proteins. The encoded protein is a multi-pass membrane protein and is thought to form a receptor-activated non-selective calcium permeant cation channel. The protein is active alone or as a heteromultimeric assembly with TRPC1, TRPC3, and TRPC4. It also interacts with multiple proteins including calmodulin, CABP1, enkurin, Na(+)-H+ exchange regulatory factor (NHERF ), interferon-induced GTP-binding protein (MX1), ring finger protein 24 (RNF24), and SEC14 domain and spectrin repeat-containing protein 1 (SESTD1). [provided by RefSeq, May 2010]
TRPC5 Gene-Disease associations (from GenCC):
- neurodevelopmental disorderInheritance: XL Classification: LIMITED Submitted by: G2P
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_012471.3. You can select a different transcript below to see updated ACMG assignments.
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
22
GnomAD2 exomes AF: 0.00000551 AC: 1AN: 181422 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
181422
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 9.11e-7 AC: 1AN: 1097671Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 1AN XY: 363117 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1097671
Hom.:
Cov.:
31
AF XY:
AC XY:
1
AN XY:
363117
show subpopulations
African (AFR)
AF:
AC:
0
AN:
26396
American (AMR)
AF:
AC:
0
AN:
35144
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
19349
East Asian (EAS)
AF:
AC:
0
AN:
30157
South Asian (SAS)
AF:
AC:
0
AN:
54050
European-Finnish (FIN)
AF:
AC:
0
AN:
40504
Middle Eastern (MID)
AF:
AC:
0
AN:
4116
European-Non Finnish (NFE)
AF:
AC:
0
AN:
841882
Other (OTH)
AF:
AC:
1
AN:
46073
GnomAD4 genome
GnomAD4 genome
Cov.:
22
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:no assertion criteria provided
Pathogenic
VUS
Benign
Condition
-
1
-
TRPC5-related disorder (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
M_CAP
Pathogenic
D
MetaRNN
Uncertain
T
MetaSVM
Uncertain
T
MutationAssessor
Benign
N
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Uncertain
Sift
Pathogenic
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MutPred
Loss of phosphorylation at S925 (P = 0.0404)
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
Publications
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