15-45111868-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP3

The NM_001363711.2(DUOX2):c.413C>A(p.Pro138His) 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 pathogenic 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. P138L) has been classified as Benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: DUOX2 NM_001363711.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.47

Genes affected

DUOX2 (HGNC:13273): (dual oxidase 2) The protein encoded by this gene is a glycoprotein and a member of the NADPH oxidase family. The synthesis of thyroid hormone is catalyzed by a protein complex located at the apical membrane of thyroid follicular cells. This complex contains an iodide transporter, thyroperoxidase, and a peroxide generating system that includes this encoded protein and DUOX1. This protein is known as dual oxidase because it has both a peroxidase homology domain and a gp91phox domain. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.794

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DUOX2	NM_001363711.2	c.413C>A	p.Pro138His	missense_variant	5/34	ENST00000389039.11
DUOX2	NM_014080.5	c.413C>A	p.Pro138His	missense_variant	5/34

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DUOX2	ENST00000389039.11	c.413C>A	p.Pro138His	missense_variant	5/34	1	NM_001363711.2	P4
DUOX2	ENST00000603300.1	c.413C>A	p.Pro138His	missense_variant	5/34	1		A1
DUOX2	ENST00000558383.1	n.456C>A		non_coding_transcript_exon_variant	4/17	5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 85

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Uncertain	0.012	T
BayesDel_noAF	Benign	-0.22
Cadd	Benign	22
Dann	Uncertain	0.99
DEOGEN2	Benign	0.12	T;T
Eigen	Benign	-0.081
Eigen_PC	Benign	-0.073
FATHMM_MKL	Uncertain	0.88	D
LIST_S2	Uncertain	0.89	D;D
M_CAP	Uncertain	0.089	D
MetaRNN	Pathogenic	0.79	D;D
MetaSVM	Benign	-0.67	T
MutationTaster	Benign	0.0036	P
PrimateAI	Benign	0.45	T
PROVEAN	Uncertain	-3.6	D;.
REVEL	Benign	0.14
Sift	Uncertain	0.0090	D;.
Sift4G	Uncertain	0.023	D;D
Polyphen		0.45	.;B
Vest4		0.51
MutPred		0.61		Loss of disorder (P = 0.0638);Loss of disorder (P = 0.0638);
MVP		0.66
MPC		1.2
ClinPred		0.99	D
GERP RS		1.9
Varity_R		0.28
gMVP		0.66

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: rs2001616; hg19: chr15-45404066;