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NM_024105.4(ALG12):c.1460C>T (p.Pro487Leu) AND ALG12-congenital disorder of glycosylation

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 7, 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:
RCV001967494.5

Allele description [Variation Report for NM_024105.4(ALG12):c.1460C>T (p.Pro487Leu)]

NM_024105.4(ALG12):c.1460C>T (p.Pro487Leu)

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.1460C>T (p.Pro487Leu)
HGVS:
  • NC_000022.11:g.49903845G>A
  • NG_008927.1:g.19614C>T
  • NM_024105.4:c.1460C>TMANE SELECT
  • NP_077010.1:p.Pro487Leu
  • NC_000022.10:g.50297493G>A
Protein change:
P487L
Links:
dbSNP: rs778688714
NCBI 1000 Genomes Browser:
rs778688714
Molecular consequence:
  • NM_024105.4:c.1460C>T - missense variant - [Sequence Ontology: SO:0001583]

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
SCV002207262Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Sep 7, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002207262.2

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

Description

This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 487 of the ALG12 protein (p.Pro487Leu). This variant is present in population databases (rs778688714, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with ALG12-related conditions. ClinVar contains an entry for this variant (Variation ID: 1430387). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0". The leucine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Sep 29, 2024