chr6-83125549-G-A
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_015018.4(DOP1A):c.1535G>A(p.Arg512Lys) 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 benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Consequence
DOP1A
NM_015018.4 missense
NM_015018.4 missense
Scores
3
4
8
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 9.60
Genes affected
DOP1A (HGNC:21194): (DOP1 leucine zipper like protein A) Predicted to be involved in Golgi to endosome transport and endoplasmic reticulum organization. Predicted to be located in Golgi membrane. Predicted to be active in endosome and trans-Golgi network. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.31332695).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DOP1A | NM_015018.4 | c.1535G>A | p.Arg512Lys | missense_variant | 15/39 | ENST00000349129.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOP1A | ENST00000349129.7 | c.1535G>A | p.Arg512Lys | missense_variant | 15/39 | 1 | NM_015018.4 | P4 | |
DOP1A | ENST00000369739.7 | c.1508G>A | p.Arg503Lys | missense_variant | 14/39 | 1 | A1 | ||
DOP1A | ENST00000237163.9 | c.1508G>A | p.Arg503Lys | missense_variant | 15/40 | 5 | A1 | ||
DOP1A | ENST00000604380.1 | c.287G>A | p.Arg96Lys | missense_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;.
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D
PrimateAI
Pathogenic
D
REVEL
Benign
Sift4G
Benign
T;T;T
Polyphen
0.68
.;P;.
Vest4
MutPred
0.43
.;Gain of ubiquitination at R512 (P = 0.0177);.;
MVP
MPC
0.53
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
No publications associated with this variant yet.