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NM_019109.5(ALG1):c.877T>C (p.Ser293Pro) AND ALG1-congenital disorder of glycosylation

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jun 23, 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:
RCV000625977.2

Allele description [Variation Report for NM_019109.5(ALG1):c.877T>C (p.Ser293Pro)]

NM_019109.5(ALG1):c.877T>C (p.Ser293Pro)

Gene:
ALG1:ALG1 chitobiosyldiphosphodolichol beta-mannosyltransferase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p13.3
Genomic location:
Preferred name:
NM_019109.5(ALG1):c.877T>C (p.Ser293Pro)
HGVS:
  • NC_000016.10:g.5079078T>C
  • NG_009202.1:g.12270T>C
  • NM_001330504.2:c.544T>C
  • NM_019109.5:c.877T>CMANE SELECT
  • NP_001317433.1:p.Ser182Pro
  • NP_061982.3:p.Ser293Pro
  • NC_000016.9:g.5129079T>C
Protein change:
S182P
Links:
dbSNP: rs1555452127
NCBI 1000 Genomes Browser:
rs1555452127
Molecular consequence:
  • NM_001330504.2:c.544T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_019109.5:c.877T>C - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
ALG1-congenital disorder of glycosylation
Synonyms:
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Ik; CDG Ik; Congenital disorder of glycosylation type 1K; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0012052; MedGen: C2931005; Orphanet: 79327; OMIM: 608540

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000746580Undiagnosed Diseases Network, NIH
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Jun 23, 2017) 		maternalclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
Whitematernalyes1not providednot providednot providednot providedclinical 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 Undiagnosed Diseases Network, NIH, SCV000746580.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1White1not providednot providedclinical testing PubMed (1)

Description

Clinical genome sequencing revealed 3 variants of uncertain significance in the ALG1 gene. Multiple lines of computational evidence support a deleterious effect of these variants on the gene or gene product. cDNA experiments performed on a research basis demonstrated that the paternally inherited variant (c.1187+3A>G) is damaging. The maternally inherited variants are rare and are not present in the 1000 Genomes Project nor the Exome Aggregate Consortium (ExAC) databases. Based on these findings, the clinical team elevated these variants to likely pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1maternalyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Oct 8, 2022