NM_015901.6:c.632G>T

Variant names:

• chr10-73125438-G-T
• rs144174919
• NM_015901.6:c.632G>T

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP3_Moderate

The NM_015901.6(NUDT13):​c.632G>T​(p.Arg211Leu) variant causes a missense change. 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. R211Q) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 31)
• Consequence: NUDT13 NM_015901.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.76

Genes affected

NUDT13 (HGNC:18827): (nudix hydrolase 13) Predicted to enable NADH pyrophosphatase activity. Predicted to be involved in NADH metabolic process and NADP catabolic process. Predicted to be located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000272599 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.845

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUDT13	NM_015901.6	c.632G>T	p.Arg211Leu	missense_variant	Exon 7 of 9	ENST00000357321.9	NP_056985.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUDT13	ENST00000357321.9	c.632G>T	p.Arg211Leu	missense_variant	Exon 7 of 9	5	NM_015901.6	ENSP00000349874.4

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 31

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.30
BayesDel_addAF	Pathogenic	0.26	D
BayesDel_noAF	Pathogenic	0.14
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Benign	0.021	.;.;.;T
Eigen	Uncertain	0.52
Eigen_PC	Uncertain	0.43
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Uncertain	0.95	D;D;D;D
M_CAP	Benign	0.079	D
MetaRNN	Pathogenic	0.84	D;D;D;D
MetaSVM	Benign	-0.40	T
MutationAssessor	Pathogenic	3.2	.;.;.;M
PrimateAI	Benign	0.39	T
PROVEAN	Pathogenic	-5.5	.;D;D;D
REVEL	Uncertain	0.48
Sift	Uncertain	0.0060	.;D;D;D
Sift4G	Uncertain	0.0090	D;D;D;D
Polyphen		0.97	.;.;.;D
Vest4		0.77
MutPred		0.67		Gain of stability (P = 0.0386);.;.;Gain of stability (P = 0.0386);
MVP		0.75
MPC		0.38
ClinPred		0.99	D
GERP RS		4.1
Varity_R		0.74
gMVP		0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.15		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: rs144174919; hg19: chr10-74885196;