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NM_133642.5(LARGE1):c.1827A>G (p.Ser609=) AND Muscular dystrophy-dystroglycanopathy type B6

Germline classification:
Benign (2 submissions)
Last evaluated:
Jan 31, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000560113.13

Allele description [Variation Report for NM_133642.5(LARGE1):c.1827A>G (p.Ser609=)]

NM_133642.5(LARGE1):c.1827A>G (p.Ser609=)

Gene:
LARGE1:LARGE xylosyl- and glucuronyltransferase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
22q12.3
Genomic location:
Preferred name:
NM_133642.5(LARGE1):c.1827A>G (p.Ser609=)
Other names:
p.S609S:TCA>TCG
HGVS:
  • NC_000022.11:g.33283252T>C
  • NG_009929.2:g.642177A>G
  • NM_001362949.2:c.1827A>G
  • NM_001362951.2:c.1827A>G
  • NM_001362953.2:c.1827A>G
  • NM_001378624.1:c.1827A>G
  • NM_001378625.1:c.1827A>G
  • NM_001378626.1:c.1827A>G
  • NM_001378627.1:c.1731-5997A>G
  • NM_001378628.1:c.1731-5997A>G
  • NM_001378629.1:c.1671A>G
  • NM_001378630.1:c.1224A>G
  • NM_001378631.1:c.972-5997A>G
  • NM_004737.7:c.1827A>G
  • NM_133642.5:c.1827A>GMANE SELECT
  • NP_001349878.1:p.Ser609=
  • NP_001349880.1:p.Ser609=
  • NP_001349882.1:p.Ser609=
  • NP_001365553.1:p.Ser609=
  • NP_001365554.1:p.Ser609=
  • NP_001365555.1:p.Ser609=
  • NP_001365558.1:p.Ser557=
  • NP_001365559.1:p.Ser408=
  • NP_004728.1:p.Ser609=
  • NP_598397.1:p.Ser609=
  • LRG_856t1:c.1827A>G
  • LRG_856t2:c.1827A>G
  • LRG_856:g.642177A>G
  • LRG_856p1:p.Ser609=
  • LRG_856p2:p.Ser609=
  • NC_000022.10:g.33679238T>C
  • NM_004737.4:c.1827A>G
  • NP_004728.1:p.(=)
Links:
dbSNP: rs11913417
NCBI 1000 Genomes Browser:
rs11913417
Molecular consequence:
  • NM_001378627.1:c.1731-5997A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001378628.1:c.1731-5997A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001378631.1:c.972-5997A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001362949.2:c.1827A>G - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001362951.2:c.1827A>G - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001362953.2:c.1827A>G - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001378624.1:c.1827A>G - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001378625.1:c.1827A>G - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001378626.1:c.1827A>G - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001378629.1:c.1671A>G - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001378630.1:c.1224A>G - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_004737.7:c.1827A>G - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_133642.5:c.1827A>G - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Muscular dystrophy-dystroglycanopathy type B6 (MDDGB6)
Synonyms:
MUSCULAR DYSTROPHY, CONGENITAL, LARGE-RELATED; MUSCULAR DYSTROPHY, CONGENITAL, TYPE 1D; MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH IMPAIRED INTELLECTUAL DEVELOPMENT), TYPE B, 6
Identifiers:
MONDO: MONDO:0012138; MedGen: C1837229; OMIM: 608840

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000438150Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)
Benign
(Jan 13, 2018)
germlineclinical testing

Citation Link,

SCV000638982Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Benign
(Jan 31, 2024)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 Illumina Laboratory Services, Illumina, SCV000438150.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV000638982.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 7, 2024