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NM_133642.5(LARGE1):c.309C>T (p.Ser103=) AND Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A6

Germline classification:
Likely benign (1 submission)
Last evaluated:
Apr 27, 2017
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:
RCV000320123.6

Allele description [Variation Report for NM_133642.5(LARGE1):c.309C>T (p.Ser103=)]

NM_133642.5(LARGE1):c.309C>T (p.Ser103=)

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.309C>T (p.Ser103=)
Other names:
p.S103S:TCC>TCT
HGVS:
  • NC_000022.11:g.33650466G>A
  • NG_009929.2:g.274963C>T
  • NM_001362949.2:c.309C>T
  • NM_001362951.2:c.309C>T
  • NM_001362953.2:c.309C>T
  • NM_001378624.1:c.309C>T
  • NM_001378625.1:c.309C>T
  • NM_001378626.1:c.309C>T
  • NM_001378627.1:c.309C>T
  • NM_001378628.1:c.309C>T
  • NM_001378629.1:c.309C>T
  • NM_004737.7:c.309C>T
  • NM_133642.5:c.309C>TMANE SELECT
  • NP_001349878.1:p.Ser103=
  • NP_001349880.1:p.Ser103=
  • NP_001349882.1:p.Ser103=
  • NP_001365553.1:p.Ser103=
  • NP_001365554.1:p.Ser103=
  • NP_001365555.1:p.Ser103=
  • NP_001365556.1:p.Ser103=
  • NP_001365557.1:p.Ser103=
  • NP_001365558.1:p.Ser103=
  • NP_004728.1:p.Ser103=
  • NP_598397.1:p.Ser103=
  • LRG_856t1:c.309C>T
  • LRG_856t2:c.309C>T
  • LRG_856:g.274963C>T
  • LRG_856p1:p.Ser103=
  • LRG_856p2:p.Ser103=
  • NC_000022.10:g.34046452G>A
  • NM_004737.4:c.309C>T
  • NP_004728.1:p.(=)
Links:
dbSNP: rs59349720
NCBI 1000 Genomes Browser:
rs59349720
Molecular consequence:
  • NM_001362949.2:c.309C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001362951.2:c.309C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001362953.2:c.309C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001378624.1:c.309C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001378625.1:c.309C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001378626.1:c.309C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001378627.1:c.309C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001378628.1:c.309C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001378629.1:c.309C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_004737.7:c.309C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_133642.5:c.309C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A6
Synonyms:
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH BRAIN AND EYE ANOMALIES), TYPE A, 6; WALKER-WARBURG SYNDROME OR MUSCLE-EYE-BRAIN DISEASE, LARGE-RELATED
Identifiers:
MONDO: MONDO:0013158; MedGen: C3150414; Orphanet: 588; Orphanet: 899; OMIM: 613154

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000438175Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)		Likely benign
(Apr 27, 2017) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000438175.3

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

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

Last Updated: May 16, 2025