17-17206004-C-A
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_178836.4(PLD6):c.283G>T(p.Asp95Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PLD6
NM_178836.4 missense
NM_178836.4 missense
Scores
3
10
5
Clinical Significance
Conservation
PhyloP100: 2.48
Publications
0 publications found
Genes affected
PLD6 (HGNC:30447): (phospholipase D family member 6) Enables cardiolipin hydrolase activity and protein homodimerization activity. Involved in mitochondrial fusion. Acts upstream of or within positive regulation of mitochondrial fusion. Located in mitochondrial outer membrane. [provided by Alliance of Genome Resources, Apr 2022]
ENSG00000264187 (HGNC:):
MPRIP (HGNC:30321): (myosin phosphatase Rho interacting protein) Enables cadherin binding activity. Predicted to be involved in actin filament organization. Located in actin cytoskeleton and cytosol. [provided by Alliance of Genome Resources, Apr 2022]
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_178836.4. 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 |
|---|---|---|---|---|---|---|---|---|---|
| PLD6 | TSL:1 MANE Select | c.283G>T | p.Asp95Tyr | missense | Exon 1 of 2 | ENSP00000317177.3 | Q8N2A8 | ||
| ENSG00000264187 | TSL:1 | n.*417+1021G>T | intron | N/A | ENSP00000394249.3 | J3QW42 | |||
| MPRIP | TSL:3 | c.*17+4371C>A | intron | N/A | ENSP00000464276.1 | J3QRL2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1396190Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 689476
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1396190
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
689476
African (AFR)
AF:
AC:
0
AN:
31706
American (AMR)
AF:
AC:
0
AN:
36306
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25106
East Asian (EAS)
AF:
AC:
0
AN:
36092
South Asian (SAS)
AF:
AC:
0
AN:
79536
European-Finnish (FIN)
AF:
AC:
0
AN:
42354
Middle Eastern (MID)
AF:
AC:
0
AN:
5358
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1081666
Other (OTH)
AF:
AC:
0
AN:
58066
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Uncertain
D
MetaRNN
Uncertain
D
MetaSVM
Uncertain
T
MutationAssessor
Uncertain
M
PhyloP100
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MutPred
Loss of disorder (P = 0.0448)
MVP
MPC
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
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