5-142005065-A-T

Variant names:

• chr5-142005065-A-T
• rs1561571315
• NM_005471.5:c.461T>A

Variant summary

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

The NM_005471.5(GNPDA1):​c.461T>A​(p.Val154Glu) variant causes a missense change. The variant allele was found at a frequency of 0.000000685 in 1,460,344 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V154M) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: GNPDA1 NM_005471.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 7.15

Genes affected

GNPDA1 (HGNC:4417): (glucosamine-6-phosphate deaminase 1) Glucosamine-6-phosphate deaminase (EC 3.5.99.6) is an allosteric enzyme that catalyzes the reversible conversion of D-glucosamine-6-phosphate into D-fructose-6-phosphate and ammonium (Arreola et al., 2003 [PubMed 12965206]).[supplied by OMIM, Jan 2010]

ACMG classification

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 rank	MANE	Protein	UniProt
GNPDA1	NM_005471.5	c.461T>A	p.Val154Glu	missense_variant	Exon 5 of 7	ENST00000311337.11	NP_005462.1
GNPDA1	XM_005268348.2	c.548T>A	p.Val183Glu	missense_variant	Exon 5 of 7		XP_005268405.1
GNPDA1	XM_006714747.2	c.461T>A	p.Val154Glu	missense_variant	Exon 6 of 8		XP_006714810.1
GNPDA1	XM_047416582.1	c.461T>A	p.Val154Glu	missense_variant	Exon 6 of 8		XP_047272538.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GNPDA1	ENST00000311337.11	c.461T>A	p.Val154Glu	missense_variant	Exon 5 of 7	1	NM_005471.5	ENSP00000311876.6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.85e-7 AC: 1 AN: 1460344 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 726214

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Feb 06, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.461T>A (p.V154E) alteration is located in exon 5 (coding exon 4) of the GNPDA1 gene. This alteration results from a T to A substitution at nucleotide position 461, causing the valine (V) at amino acid position 154 to be replaced by a glutamic acid (E). 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	0.50
BayesDel_addAF	Pathogenic	0.21	D
BayesDel_noAF	Uncertain	0.070
CADD	Uncertain	25
DANN	Benign	0.97
DEOGEN2	Benign	0.022	T;T;T;T;T;T;T;.
Eigen	Benign	0.00064
Eigen_PC	Benign	0.20
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Uncertain	0.96	D;.;.;.;D;D;D;D
M_CAP	Benign	0.026	D
MetaRNN	Uncertain	0.53	D;D;D;D;D;D;D;D
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.3	.;L;L;L;L;.;.;.
PrimateAI	Pathogenic	0.81	D
PROVEAN	Uncertain	-2.4	N;N;N;N;N;N;N;D
REVEL	Uncertain	0.33
Sift	Benign	0.35	T;T;T;T;T;T;T;T
Sift4G	Benign	0.55	T;T;T;T;T;T;.;.
Polyphen		0.012	.;B;B;B;B;.;.;.
Vest4		0.89
MutPred		0.50		Gain of disorder (P = 0.0101);Gain of disorder (P = 0.0101);Gain of disorder (P = 0.0101);Gain of disorder (P = 0.0101);Gain of disorder (P = 0.0101);Gain of disorder (P = 0.0101);.;Gain of disorder (P = 0.0101);
MVP		0.56
MPC		0.76
ClinPred		0.92	D
GERP RS		4.7
Varity_R		0.76
gMVP		0.88

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: rs1561571315; hg19: chr5-141384630;