NM_000262.3(NAGA):c.1097_1098del (p.Ile365_Tyr366insTer) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 12, 2018
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:: RCV000825989.4

Allele description [Variation Report for NM_000262.3(NAGA):c.1097_1098del (p.Ile365_Tyr366insTer)]

NM_000262.3(NAGA):c.1097_1098del (p.Ile365_Tyr366insTer)

Gene:

NAGA:alpha-N-acetylgalactosaminidase [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

22q13.2

Genomic location:

Preferred name:

NM_000262.3(NAGA):c.1097_1098del (p.Ile365_Tyr366insTer)

HGVS:

NC_000022.11:g.42060927AT[2]
NC_000022.11:g.42060927_42060928AT[2]
NG_009247.1:g.14911AT[2]
NM_000262.3:c.1097_1098delMANE SELECT
NM_001362848.1:c.1097_1098del
NM_001362850.1:c.1097_1098del
NP_000253.1:p.Ile365_Tyr366insTer
NP_001349777.1:p.Ile365_Tyr366insTer
NP_001349779.1:p.Ile365_Tyr366insTer
NC_000022.10:g.42456931AT[2]
NC_000022.10:g.42456931_42456932delAT
NM_000262.2:c.1097_1098delAT
p.Tyr366X

Links:

dbSNP: rs1602490557

NCBI 1000 Genomes Browser:

rs1602490557

Molecular consequence:

NM_000262.3:c.1097_1098del - nonsense - [Sequence Ontology: SO:0001587]
NM_001362848.1:c.1097_1098del - nonsense - [Sequence Ontology: SO:0001587]
NM_001362850.1:c.1097_1098del - nonsense - [Sequence Ontology: SO:0001587]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000967477	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Uncertain significance (Sep 12, 2018)	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

SCV000967477

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Uncertain significance
(Sep 12, 2018)

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	not provided	1	1	not provided	not provided	not provided	clinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000967477.1

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

Description

The p.Tyr366X variant in NAGA has not been previously reported in individuals wi th disease and was absent from large population studies. This frameshift variant leads to a premature termination codon at position 366. This alteration occurs within the terminal 50 bases of the second to last exon and is more likely to es cape nonsense mediated decay (NMD) and result in a truncated protein. Biallelic variants in the NAGA gene have been associated with Schindler disease, though th e evidence for a causal implication of the gene is moderate. In summary, the cli nical significance of the p.Tyr366X variant is uncertain. ACMG/AMP Criteria appl ied: PM2, PVS1_Supporting.

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

Last Updated: Dec 24, 2022

ClinVar

Relating variation to medicine