Variant 1-159782229-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001319658.2(DUSP23):c.344G>T(p.Gly115Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,461,886 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000048 ( 0 hom. )

Consequence

DUSP23
NM_001319658.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.46

Variant links:

Genes affected

DUSP23 (HGNC:21480): (dual specificity phosphatase 23) Enables protein tyrosine/serine/threonine phosphatase activity. Involved in dephosphorylation. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

DUSP23 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DUSP23	NM_001319658.2 linkuse as main transcript	c.344G>T	p.Gly115Val	missense_variant	2/2	ENST00000368107.2	NP_001306587.1	Q9BVJ7A0A140VJI5
DUSP23	NM_001319659.2 linkuse as main transcript	c.344G>T	p.Gly115Val	missense_variant	3/3		NP_001306588.1	Q9BVJ7A0A140VJI5
DUSP23	NM_017823.5 linkuse as main transcript	c.344G>T	p.Gly115Val	missense_variant	3/3		NP_060293.2	Q9BVJ7A0A140VJI5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
DUSP23	ENST00000368107.2 linkuse as main transcript	c.344G>T	p.Gly115Val	missense_variant	2/2	1	NM_001319658.2	ENSP00000357087.1	Q9BVJ7
DUSP23	ENST00000368108.7 linkuse as main transcript	c.344G>T	p.Gly115Val	missense_variant	3/3	1		ENSP00000357088.3	Q9BVJ7
DUSP23	ENST00000368109.5 linkuse as main transcript	c.344G>T	p.Gly115Val	missense_variant	3/3	2		ENSP00000357089.1	Q9BVJ7

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000479

AC:

AN:

1461886

Hom.:

Cov.:

AF XY:

0.00000688

AC XY:

AN XY:

727244

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000629

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ExAC

AF:

0.00000824

AC:

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

Sep 12, 2024

The c.344G>T (p.G115V) alteration is located in exon 3 (coding exon 2) of the DUSP23 gene. This alteration results from a G to T substitution at nucleotide position 344, causing the glycine (G) at amino acid position 115 to be replaced by a valine (V). 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

0.47

BayesDel_addAF

Benign

-0.0099

BayesDel_noAF

Benign

-0.25

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Uncertain

0.53

D;D;D

Eigen

Benign

-0.29

Eigen_PC

Benign

-0.44

FATHMM_MKL

Benign

0.20

LIST_S2

Benign

0.70

.;.;T

M_CAP

Uncertain

0.099

MetaRNN

Uncertain

0.58

D;D;D

MetaSVM

Benign

-0.55

MutationAssessor

Uncertain

2.3

M;M;M

PrimateAI

Benign

0.44

PROVEAN

Uncertain

-3.4

D;D;D

REVEL

Benign

0.28

Sift

Benign

0.074

T;T;T

Sift4G

Benign

0.15

T;T;T

Polyphen

0.99

D;D;D

Vest4

0.33

MutPred

0.55

Gain of ubiquitination at K112 (P = 0.1725);Gain of ubiquitination at K112 (P = 0.1725);Gain of ubiquitination at K112 (P = 0.1725);

MVP

0.99

MPC

0.55

ClinPred

0.78

GERP RS

2.4

Varity_R

0.27

gMVP

0.68

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.27

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.27

Position offset: 12

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over