3-25719514-TA-T

Variant names:

• chr3-25719514-TA-T
• rs1135401730
• NM_018297.4:c.1910delT

Variant summary

Our verdict is Likely pathogenic. The variant received 6 ACMG points: 6P and 0B. PVS1_Moderate PM2 PP5_Moderate

The NM_018297.4(NGLY1):​c.1910delT​(p.Leu637fs) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: NGLY1 NM_018297.4 frameshift
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:2
• Conservation: PhyloP100: 5.97
• Publications: 6 publications found

Genes affected

NGLY1 (HGNC:17646): (N-glycanase 1) This gene encodes an enzyme that catalyzes hydrolysis of an N(4)-(acetyl-beta-D-glucosaminyl) asparagine residue to N-acetyl-beta-D-glucosaminylamine and a peptide containing an aspartate residue. The encoded enzyme may play a role in the proteasome-mediated degradation of misfolded glycoproteins. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Feb 2009]

NGLY1 Gene-Disease associations (from GenCC):

• congenital disorder of deglycosylation 1

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), G2P
• NGLY1-deficiency

  Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, PanelApp Australia

ACMG classification

Our verdict: Likely_pathogenic. The variant received 6 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.028 CDS is truncated, and there are 3 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 3-25719514-TA-T is Pathogenic according to our data. Variant chr3-25719514-TA-T is described in ClinVar as Likely_pathogenic. ClinVar VariationId is 221582.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018297.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NGLY1	NM_018297.4	MANE Select	c.1910delT	p.Leu637fs	frameshift	Exon 12 of 12	NP_060767.2
	NGLY1	NM_001145293.2		c.1856delT	p.Leu619fs	frameshift	Exon 12 of 12	NP_001138765.1
	NGLY1	NM_001145294.2		c.1784delT	p.Leu595fs	frameshift	Exon 12 of 12	NP_001138766.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NGLY1	ENST00000280700.10	TSL:1 MANE Select	c.1910delT	p.Leu637fs	frameshift	Exon 12 of 12	ENSP00000280700.5
	NGLY1	ENST00000428257.5	TSL:1	c.1856delT	p.Leu619fs	frameshift	Exon 12 of 12	ENSP00000387430.1
	NGLY1	ENST00000308710.9	TSL:1	c.1847delT	p.Leu616fs	frameshift	Exon 12 of 12	ENSP00000307980.5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, single submitter

Submissions by phenotype

Congenital disorder of deglycosylation Pathogenic:1

Jan 07, 2016

Medical Biochemical Genetics, National Human Genome institute, NIH, National Institutes of Health

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

not provided Pathogenic:1

Mar 21, 2019

GeneDx

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

A variant that is likely pathogenic has been identified in the NGLY1 gene. The L637X variant has been previously reported in a patient with a clinical diagnosis of NGLY1-CDDG who had a second variant on the opposite allele (Lam et al., 2017; Kong et al., 2017). The L637X variant is not observed in large population cohorts (Lek et al., 2016). L637X is predicted to cause loss of normal protein function through protein truncation as the last 18 amino acids are lost. Therefore, this variant is likely pathogenic; however, the possibility that it is benign cannot be excluded.

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		6.0
Mutation Taster		=1/199	disease causing (ClinVar)

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

Other links and lift over

dbSNP: rs1135401730; hg19: chr3-25761005;