NM_018297.4(NGLY1):c.978_980del (p.Glu326_Ala327delinsAsp) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jan 3, 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:: RCV000483669.4

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)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000573961	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Jan 3, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000573961

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Jan 3, 2022)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000573961.6

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

Description

Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In-frame deletion of two amino acids and insertion of one amino acid in a non-repeat region; In silico analysis supports a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

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

Last Updated: Sep 29, 2024

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