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NM_024105.4(ALG12):c.160C>T (p.Gln54Ter) AND ALG12-congenital disorder of glycosylation

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 26, 2022
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:
RCV003608001.1

Allele description [Variation Report for NM_024105.4(ALG12):c.160C>T (p.Gln54Ter)]

NM_024105.4(ALG12):c.160C>T (p.Gln54Ter)

Gene:
ALG12:ALG12 alpha-1,6-mannosyltransferase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
22q13.33
Genomic location:
Preferred name:
NM_024105.4(ALG12):c.160C>T (p.Gln54Ter)
HGVS:
  • NC_000022.11:g.49913606G>A
  • NG_008927.1:g.9853C>T
  • NM_024105.4:c.160C>TMANE SELECT
  • NP_077010.1:p.Gln54Ter
  • NP_077010.1:p.Gln54Ter
  • NC_000022.10:g.50307254G>A
  • NM_024105.3:c.160C>T
Protein change:
Q54*
Molecular consequence:
  • NM_024105.4:c.160C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
ALG12-congenital disorder of glycosylation (CDG1G)
Synonyms:
CDG Ig; CDG 1G; Congenital disorder of glycosylation, type Ig; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0011783; MedGen: C2931001; Orphanet: 79324; OMIM: 607143

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004423300Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Dec 26, 2022) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Molecular and clinical description of the first US patients with congenital disorder of glycosylation Ig.

Eklund EA, Newell JW, Sun L, Seo NS, Alper G, Willert J, Freeze HH.

Mol Genet Metab. 2005 Jan;84(1):25-31. Epub 2004 Nov 11.

PubMed [citation]
PMID:
15639192

Complex phenotypes in ALG12-congenital disorder of glycosylation (ALG12-CDG): Case series and review of the literature.

Tahata S, Gunderson L, Lanpher B, Morava E.

Mol Genet Metab. 2019 Dec;128(4):409-414. doi: 10.1016/j.ymgme.2019.08.007. Epub 2019 Aug 26. Review.

PubMed [citation]
PMID:
31481313
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV004423300.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. This variant has not been reported in the literature in individuals affected with ALG12-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gln54*) in the ALG12 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ALG12 are known to be pathogenic (PMID: 15639192, 31481313).

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

Last Updated: Feb 28, 2024