NM_001382.4(DPAGT1):c.85A>T (p.Ile29Phe) AND Congenital myasthenic syndrome 13

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jun 24, 2023
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:: RCV003236665.1

Allele description [Variation Report for NM_001382.4(DPAGT1):c.85A>T (p.Ile29Phe)]

NM_001382.4(DPAGT1):c.85A>T (p.Ile29Phe)

Genes:

LOC126861360:BRD4-independent group 4 enhancer GRCh37_chr11:118972216-118973415 [Gene]
DPAGT1:dolichyl-phosphate N-acetylglucosaminephosphotransferase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q23.3

Genomic location:

Preferred name:

NM_001382.4(DPAGT1):c.85A>T (p.Ile29Phe)

HGVS:

NC_000011.10:g.119101571T>A
NG_008918.1:g.5505A>T
NM_001382.4:c.85A>TMANE SELECT
NP_001373.2:p.Ile29Phe
NC_000011.9:g.118972281T>A
NM_001382.3:c.85A>T

Protein change:

I29F; ILE29PHE

Links:

OMIM: 191350.0010; dbSNP: rs397515328

NCBI 1000 Genomes Browser:

rs397515328

Molecular consequence:

NM_001382.4:c.85A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Congenital myasthenic syndrome 13 (CMS13)
Synonyms:: Myasthenic syndrome, congenital, with tubular aggregates 2; Myasthenic syndrome, congenital, 13, with tubular aggregates
Identifiers:: MONDO: MONDO:0013883; MedGen: C3553645; Orphanet: 353327; Orphanet: 590; OMIM: 614750

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003935143	Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jun 24, 2023)	inherited	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

SCV003935143

Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jun 24, 2023)

inherited

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	inherited	yes	not provided	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 Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, SCV003935143.1

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

Description

The heterozygous variant c.85A>T (p.Ile29Phe) has been observed in a proband with motor developmental delay, frequent falls with gait abnormalities, myopathic facies, hypotonia and mild lordotic pressure in a compound heterozygous state with the other variant c.1139C>T (p.Thr380Ile). This variant is observed in 0.0103% gnomAD (aggregated) database (PM2_moderate). DPAGT1 has low rate of benign missense variants with 22 reported pathogenic missense variants (PP2_supporting). It has been previously reported PMID: 25500013 (PP5_supporting)

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

Last Updated: Mar 5, 2024

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