NM_000262.3(NAGA):c.418C>T (p.Gln140Ter) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Apr 17, 2020
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:: RCV001508023.5

Allele description [Variation Report for NM_000262.3(NAGA):c.418C>T (p.Gln140Ter)]

NM_000262.3(NAGA):c.418C>T (p.Gln140Ter)

Genes:

LOC126863160:CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:42462918-42464117 [Gene]
NAGA:alpha-N-acetylgalactosaminidase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q13.2

Genomic location:

Preferred name:

NM_000262.3(NAGA):c.418C>T (p.Gln140Ter)

HGVS:

NC_000022.11:g.42067197G>A
NG_009247.1:g.8646C>T
NM_000262.3:c.418C>TMANE SELECT
NM_001362848.1:c.418C>T
NM_001362850.1:c.418C>T
NP_000253.1:p.Gln140Ter
NP_001349777.1:p.Gln140Ter
NP_001349779.1:p.Gln140Ter
NC_000022.10:g.42463201G>A
NM_000262.2:c.418C>T
p.Gln140*

Protein change:

Q140*

Links:

dbSNP: rs776149537

NCBI 1000 Genomes Browser:

rs776149537

Molecular consequence:

NM_000262.3:c.418C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001362848.1:c.418C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001362850.1:c.418C>T - nonsense - [Sequence Ontology: SO:0001587]

Observations:

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
SCV001713916	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Apr 17, 2020)	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

SCV001713916

Mayo Clinic Laboratories, Mayo Clinic

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Apr 17, 2020)

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	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Mayo Clinic Laboratories, Mayo Clinic, SCV001713916.1

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

Description

PVS1, PM2

#	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		1	not provided	not provided	not provided

Last Updated: Dec 24, 2023

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