7-76480765-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001102594.3(DTX2):​c.256C>T​(p.Arg86Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000523 in 1,604,742 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000033 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000054 ( 0 hom. )

Consequence

DTX2
NM_001102594.3 missense

Scores

7
9
3

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.58
Variant links:
Genes affected
DTX2 (HGNC:15973): (deltex E3 ubiquitin ligase 2) DTX2 functions as an E3 ubiquitin ligase (Takeyama et al., 2003 [PubMed 12670957]).[supplied by OMIM, Nov 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High AC in GnomAd4 at 5 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
DTX2NM_001102594.3 linkc.256C>T p.Arg86Cys missense_variant 3/11 ENST00000430490.7 NP_001096064.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DTX2ENST00000430490.7 linkc.256C>T p.Arg86Cys missense_variant 3/111 NM_001102594.3 ENSP00000411986.2 Q86UW9-1

Frequencies

GnomAD3 genomes
AF:
0.0000328
AC:
5
AN:
152236
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0000482
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000156
AC:
37
AN:
237154
Hom.:
0
AF XY:
0.0000773
AC XY:
10
AN XY:
129414
show subpopulations
Gnomad AFR exome
AF:
0.0000673
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000501
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000144
Gnomad NFE exome
AF:
0.000226
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000544
AC:
79
AN:
1452388
Hom.:
0
Cov.:
31
AF XY:
0.0000471
AC XY:
34
AN XY:
721666
show subpopulations
Gnomad4 AFR exome
AF:
0.0000603
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000202
Gnomad4 SAS exome
AF:
0.0000819
Gnomad4 FIN exome
AF:
0.000113
Gnomad4 NFE exome
AF:
0.0000434
Gnomad4 OTH exome
AF:
0.000117
GnomAD4 genome
AF:
0.0000328
AC:
5
AN:
152354
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
74502
show subpopulations
Gnomad4 AFR
AF:
0.0000481
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000275
Hom.:
0
Bravo
AF:
0.0000604
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.000231
AC:
28

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 submitterclinical testingAmbry GeneticsJun 05, 2023The c.256C>T (p.R86C) alteration is located in exon 4 (coding exon 1) of the DTX2 gene. This alteration results from a C to T substitution at nucleotide position 256, causing the arginine (R) at amino acid position 86 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.49
BayesDel_addAF
Uncertain
0.019
T
BayesDel_noAF
Uncertain
0.13
CADD
Pathogenic
30
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.36
T;T;T;T;T;T;T;.
Eigen
Pathogenic
0.69
Eigen_PC
Pathogenic
0.67
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Pathogenic
1.0
.;.;D;.;D;D;D;D
M_CAP
Uncertain
0.10
D
MetaRNN
Uncertain
0.69
D;D;D;D;D;D;D;D
MetaSVM
Benign
-0.55
T
MutationAssessor
Uncertain
2.5
M;M;.;.;M;.;.;M
PrimateAI
Pathogenic
0.87
D
PROVEAN
Pathogenic
-6.4
D;D;D;D;D;D;D;D
REVEL
Uncertain
0.42
Sift
Uncertain
0.0030
D;D;D;D;D;D;D;D
Sift4G
Pathogenic
0.0010
D;D;D;D;D;D;D;D
Polyphen
1.0
D;D;.;.;D;.;.;D
Vest4
0.94
MVP
0.84
MPC
1.1
ClinPred
0.46
T
GERP RS
5.5
Varity_R
0.59
gMVP
0.73

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs370872905; hg19: chr7-76110082; COSMIC: COSV100184300; COSMIC: COSV100184300; API