NM_001099922.3(ALG13):c.1886A>G (p.Tyr629Cys) AND Developmental and epileptic encephalopathy, 36

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 29, 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:: RCV003653795.2

Allele description [Variation Report for NM_001099922.3(ALG13):c.1886A>G (p.Tyr629Cys)]

NM_001099922.3(ALG13):c.1886A>G (p.Tyr629Cys)

Gene:

ALG13:ALG13 UDP-N-acetylglucosaminyltransferase subunit [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xq23

Genomic location:

Preferred name:

NM_001099922.3(ALG13):c.1886A>G (p.Tyr629Cys)

HGVS:

NC_000023.11:g.111726965A>G
NG_016238.1:g.50848A>G
NM_001039210.2:c.1886A>G
NM_001099922.3:c.1886A>GMANE SELECT
NM_001257230.2:c.1574A>G
NM_001257231.2:c.1652A>G
NM_001257234.2:c.1574A>G
NM_001257237.2:c.1574A>G
NM_001324292.2:c.1886A>G
NM_001324293.1:c.1400A>G
NP_001034299.2:p.Tyr629Cys
NP_001093392.1:p.Tyr629Cys
NP_001244159.1:p.Tyr525Cys
NP_001244160.1:p.Tyr551Cys
NP_001244163.1:p.Tyr525Cys
NP_001244166.1:p.Tyr525Cys
NP_001311221.1:p.Tyr629Cys
NP_001311222.1:p.Tyr467Cys
NC_000023.10:g.110970193A>G
NR_148693.2:n.1614A>G

Protein change:

Y467C

Molecular consequence:

NM_001039210.2:c.1886A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001099922.3:c.1886A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001257230.2:c.1574A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001257231.2:c.1652A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001257234.2:c.1574A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001257237.2:c.1574A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001324292.2:c.1886A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001324293.1:c.1400A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_148693.2:n.1614A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Developmental and epileptic encephalopathy, 36 (DEE36)
Synonyms:: Epileptic encephalopathy, early infantile, 36; Congenital disorder of glycosylation, type Is; ALG13-CDG
Identifiers:: MONDO: MONDO:0010472; MedGen: C4317295; Orphanet: 324422; OMIM: 300884

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004461532	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 29, 2023)	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

SCV004461532

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 29, 2023)

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV004461532.1

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

Description

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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt ALG13 protein function. This variant has not been reported in the literature in individuals affected with ALG13-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 629 of the ALG13 protein (p.Tyr629Cys).

#	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: Nov 30, 2024

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