NM_018297.4(NGLY1):c.978_980del (p.Glu326_Ala327delinsAsp) AND Congenital disorder of deglycosylation

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 9, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001341093.3

Allele description [Variation Report for NM_018297.4(NGLY1):c.978_980del (p.Glu326_Ala327delinsAsp)]

NM_018297.4(NGLY1):c.978_980del (p.Glu326_Ala327delinsAsp)

Gene:

NGLY1:N-glycanase 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

3p24.2

Genomic location:

Preferred name:

NM_018297.4(NGLY1):c.978_980del (p.Glu326_Ala327delinsAsp)

HGVS:

NC_000003.12:g.25737357_25737359del
NG_034108.1:g.57681_57683del
NM_001145293.2:c.978_980del
NM_001145294.2:c.852_854del
NM_001145295.2:c.978_980del
NM_018297.4:c.978_980delMANE SELECT
NP_001138765.1:p.Glu326_Ala327delinsAsp
NP_001138766.1:p.Glu284_Ala285delinsAsp
NP_001138767.1:p.Glu326_Ala327delinsAsp
NP_060767.2:p.Glu326_Ala327delinsAsp
NC_000003.11:g.25778848_25778850del
NM_018297.3:c.978_980del
NM_018297.3:c.978_980delAGC

Links:

dbSNP: rs761634625

NCBI 1000 Genomes Browser:

rs761634625

Molecular consequence:

NM_001145293.2:c.978_980del - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001145294.2:c.852_854del - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001145295.2:c.978_980del - inframe_indel - [Sequence Ontology: SO:0001820]
NM_018297.4:c.978_980del - inframe_indel - [Sequence Ontology: SO:0001820]

Condition(s)

Name:: Congenital disorder of deglycosylation (CDDG)
Identifiers:: MONDO: MONDO:0031376; MedGen: C3808991; OMIM: PS615273

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001534941	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 9, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001534941

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 9, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001534941.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This variant, c.978_980del, is a complex sequence change that results in the deletion of 2 amino acids and insertion of 1 amino acid(s) in the NGLY1 protein (p.Glu326_Ala327delinsAsp). This variant is present in population databases (rs761634625, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with NGLY1-related conditions. ClinVar contains an entry for this variant (Variation ID: 424175). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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