rs945418632

Variant names:

• chr17-82036950-C-G
• rs945418632
• NM_016286.4:c.214G>C

Your query was ambiguous. Multiple possible variants found:

• chr17-82036950-C-G
• chr17-82036950-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_016286.4(DCXR):​c.214G>C​(p.Gly72Arg) 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.

• Frequency: Genomes: not found (cov: 33)
• Consequence: DCXR NM_016286.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.705

Genes affected

DCXR (HGNC:18985): (dicarbonyl and L-xylulose reductase) The protein encoded by this gene acts as a homotetramer to catalyze diacetyl reductase and L-xylulose reductase reactions. The encoded protein may play a role in the uronate cycle of glucose metabolism and in the cellular osmoregulation in the proximal renal tubules. Defects in this gene are a cause of pentosuria. Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Aug 2010]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.086269975).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCXR	NM_016286.4	c.214G>C	p.Gly72Arg	missense_variant	Exon 3 of 8	ENST00000306869.7	NP_057370.1
DCXR	NM_001195218.1	c.208G>C	p.Gly70Arg	missense_variant	Exon 3 of 8		NP_001182147.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCXR	ENST00000306869.7	c.214G>C	p.Gly72Arg	missense_variant	Exon 3 of 8	1	NM_016286.4	ENSP00000303356.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.15
BayesDel_addAF	Benign	-0.033	T
BayesDel_noAF	Benign	-0.28
CADD	Benign	3.5
DANN	Benign	0.61
DEOGEN2	Benign	0.033	.;T;T;T
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.066	N
LIST_S2	Uncertain	0.86	D;D;T;D
M_CAP	Benign	0.033	D
MetaRNN	Benign	0.086	T;T;T;T
MetaSVM	Benign	-0.97	T
MutationAssessor	Benign	0.24	.;N;.;.
PrimateAI	Benign	0.43	T
PROVEAN	Benign	-1.3	.;N;.;.
REVEL	Benign	0.035
Sift	Benign	0.57	.;T;.;.
Sift4G	Benign	0.17	T;T;.;T
Polyphen		0.0010	.;B;.;.
Vest4		0.13
MutPred		0.42		.;Gain of solvent accessibility (P = 0.0306);.;.;
MVP		0.53
MPC		0.42
ClinPred		0.037	T
GERP RS		-1.6
RBP_binding_hub_radar		0.97
RBP_regulation_power_radar		2.1
Varity_R		0.070
gMVP		0.57

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs945418632; hg19: chr17-79994826;