NM_133642.5(LARGE1):c.309C>T (p.Ser103=) AND Muscular dystrophy-dystroglycanopathy type B6

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Feb 1, 2025
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:: RCV000544713.17

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 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000438174	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Apr 27, 2017)	germline	clinical testing	Citation Link,
SCV000638998	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Feb 1, 2025)	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

SCV000438174

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Apr 27, 2017)

germline

clinical testing

Citation Link,

SCV000638998

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Feb 1, 2025)

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	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV000438174.3

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

#	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		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000638998.9

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

#	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		not provided	not provided	not provided	not provided

Last Updated: May 16, 2025

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