rs3088142

Positions:

• chr10-75094806-C-G
• chr10-75094806-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001363514.2(DUSP13):​c.875G>C​(p.Cys292Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 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. C292Y) has been classified as Benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: DUSP13 NM_001363514.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236

Genes affected

DUSP13 (HGNC:):

DUSP13B (HGNC:19681): (dual specificity phosphatase 13B) Members of the protein-tyrosine phosphatase superfamily cooperate with protein kinases to regulate cell proliferation and differentiation. This gene encodes a dual specificity phosphatase that acts on both phosphotyrosine and phosphoserine/threonine residues. The encoded protein is expressed in testis. [provided by RefSeq, Mar 2023]

DUSP13A (HGNC:56772): (dual specificity phosphatase 13A) Members of the protein-tyrosine phosphatase superfamily cooperate with protein kinases to regulate cell proliferation and differentiation. This gene encodes a dual specificity phosphatase that acts on both phosphotyrosine and phosphoserine/threonine residues. The encoded protein is expressed in skeletal muscle. [provided by RefSeq, Mar 2023]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.040029317).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DUSP13	NM_001363514.2	c.875G>C	p.Cys292Ser	missense_variant	4/4	ENST00000478873.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DUSP13B	ENST00000478873.7	c.875G>C	p.Cys292Ser	missense_variant	4/4	5	NM_001363514.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 57

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.25
BayesDel_addAF	Benign	-0.10	T
BayesDel_noAF	Benign	-0.38
CADD	Benign	7.0
DANN	Benign	0.76
DEOGEN2	Benign	0.19	T;T;T;.;T;T;.
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.32	N
M_CAP	Uncertain	0.089	D
MetaRNN	Benign	0.040	T;T;T;T;T;T;T
MetaSVM	Benign	-0.87	T
MutationAssessor	Benign	-0.53	N;N;.;.;.;N;.
MutationTaster	Benign	0.97	P;P;P;P;P;P;P
PrimateAI	Benign	0.27	T
PROVEAN	Benign	-1.6	N;.;N;.;.;.;N
REVEL	Benign	0.21
Sift	Benign	0.28	T;.;T;.;.;.;T
Sift4G	Benign	0.39	T;T;T;T;T;T;T
Polyphen		0.043	B;B;.;.;.;B;B
Vest4		0.24
MVP		0.048
MPC		0.20
ClinPred		0.11	T
GERP RS		-2.2
Varity_R		0.17
gMVP		0.56

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

Other links and lift over

dbSNP: rs3088142; hg19: chr10-76854564;