chr17-66884565-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_145811.3(CACNG5):c.474T>G(p.Asp158Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00028 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CACNG5
NM_145811.3 missense
NM_145811.3 missense
Scores
2
6
10
Clinical Significance
Conservation
PhyloP100: -2.77
Genes affected
CACNG5 (HGNC:1409): (calcium voltage-gated channel auxiliary subunit gamma 5) The protein encoded by this gene is a type II transmembrane AMPA receptor regulatory protein (TARP). TARPs regulate both trafficking and channel gating of the AMPA receptors. This gene is part of a functionally diverse eight-member protein subfamily of the PMP-22/EMP/MP20 family and is located in a cluster with two family members, a type I TARP and a calcium channel gamma subunit. This gene is a susceptibility locus for schizophrenia and bipolar disorder. [provided by RefSeq, Dec 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNG5 | NM_145811.3 | c.474T>G | p.Asp158Glu | missense_variant | 5/6 | ENST00000533854.6 | |
CACNG5 | NM_001371476.1 | c.424+3868T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNG5 | ENST00000533854.6 | c.474T>G | p.Asp158Glu | missense_variant | 5/6 | 2 | NM_145811.3 | P1 | |
CACNG5 | ENST00000307139.4 | c.474T>G | p.Asp158Glu | missense_variant | 4/5 | 1 | P1 | ||
CACNG5 | ENST00000673855.1 | c.424+3868T>G | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 152002Hom.: 0 Cov.: 32 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000281 AC: 408AN: 1451098Hom.: 0 Cov.: 30 AF XY: 0.000260 AC XY: 188AN XY: 722280
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GnomAD4 genome ? Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 152002Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74246
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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 | Dec 17, 2023 | The c.474T>G (p.D158E) alteration is located in exon 4 (coding exon 4) of the CACNG5 gene. This alteration results from a T to G substitution at nucleotide position 474, causing the aspartic acid (D) at amino acid position 158 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Uncertain
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
M_CAP
Uncertain
D
MetaRNN
Uncertain
D;D
MetaSVM
Uncertain
T
MutationAssessor
Benign
L;L
MutationTaster
Benign
D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;N
REVEL
Uncertain
Sift
Benign
D;D
Sift4G
Benign
T;T
Polyphen
D;D
Vest4
MutPred
Gain of sheet (P = 0.0149);Gain of sheet (P = 0.0149);
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