17-75047294-G-T
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015353.3(KCTD2):c.44G>T(p.Gly15Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000662 in 151,008 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G15E) has been classified as Uncertain significance.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
KCTD2
NM_015353.3 missense
NM_015353.3 missense
Scores
2
16
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.345
Publications
0 publications found
Genes affected
KCTD2 (HGNC:21294): (potassium channel tetramerization domain containing 2) Predicted to enable cullin family protein binding activity. Predicted to be involved in proteasome-mediated ubiquitin-dependent protein catabolic process. Predicted to be part of Cul3-RING ubiquitin ligase complex. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
ATP5PD (HGNC:845): (ATP synthase peripheral stalk subunit d) Mitochondrial ATP synthase catalyzes ATP synthesis, utilizing an electrochemical gradient of protons across the inner membrane during oxidative phosphorylation. It is composed of two linked multi-subunit complexes: the soluble catalytic core, F1, and the membrane-spanning component, Fo, which comprises the proton channel. The F1 complex consists of 5 different subunits (alpha, beta, gamma, delta, and epsilon) assembled in a ratio of 3 alpha, 3 beta, and a single representative of the other 3. The Fo seems to have nine subunits (a, b, c, d, e, f, g, F6 and 8). This gene encodes the d subunit of the Fo complex. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene. In addition, three pseudogenes are located on chromosomes 9, 12 and 15. [provided by RefSeq, Jun 2010]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.16859058).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_015353.3. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| KCTD2 | TSL:1 MANE Select | c.44G>T | p.Gly15Val | missense | Exon 1 of 6 | ENSP00000312814.6 | Q14681 | ||
| KCTD2 | TSL:1 | c.-258-1926G>T | intron | N/A | ENSP00000464630.1 | J3QSC8 | |||
| KCTD2 | TSL:1 | n.44G>T | non_coding_transcript_exon | Exon 1 of 7 | ENSP00000364435.3 | H0Y3B9 |
Frequencies
GnomAD3 genomes 0.00000662 AC: 1AN: 151008Hom.: 0 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
151008
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1008996Hom.: 0 Cov.: 18 AF XY: 0.00 AC XY: 0AN XY: 477764
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1008996
Hom.:
Cov.:
18
AF XY:
AC XY:
0
AN XY:
477764
African (AFR)
AF:
AC:
0
AN:
20786
American (AMR)
AF:
AC:
0
AN:
6518
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
11890
East Asian (EAS)
AF:
AC:
0
AN:
21864
South Asian (SAS)
AF:
AC:
0
AN:
21424
European-Finnish (FIN)
AF:
AC:
0
AN:
17972
Middle Eastern (MID)
AF:
AC:
0
AN:
2582
European-Non Finnish (NFE)
AF:
AC:
0
AN:
866958
Other (OTH)
AF:
AC:
0
AN:
39002
GnomAD4 genome 0.00000662 AC: 1AN: 151008Hom.: 0 Cov.: 31 AF XY: 0.0000136 AC XY: 1AN XY: 73746 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
151008
Hom.:
Cov.:
31
AF XY:
AC XY:
1
AN XY:
73746
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41300
American (AMR)
AF:
AC:
1
AN:
15172
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3466
East Asian (EAS)
AF:
AC:
0
AN:
5140
South Asian (SAS)
AF:
AC:
0
AN:
4826
European-Finnish (FIN)
AF:
AC:
0
AN:
10082
Middle Eastern (MID)
AF:
AC:
0
AN:
312
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67720
Other (OTH)
AF:
AC:
0
AN:
2080
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Pathogenic
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
PhyloP100
PrimateAI
Pathogenic
D
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MutPred
Loss of relative solvent accessibility (P = 0.0071)
MVP
MPC
ClinPred
T
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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