NM_018389.5(SLC35C1):c.22C>T (p.Arg8Trp) AND Leukocyte adhesion deficiency type II

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 11, 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:: RCV003115099.3

Allele description [Variation Report for NM_018389.5(SLC35C1):c.22C>T (p.Arg8Trp)]

NM_018389.5(SLC35C1):c.22C>T (p.Arg8Trp)

Gene:

SLC35C1:solute carrier family 35 member C1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11p11.2

Genomic location:

Preferred name:

NM_018389.5(SLC35C1):c.22C>T (p.Arg8Trp)

HGVS:

NC_000011.10:g.45805823C>T
NG_009875.1:g.6752C>T
NM_001145265.2:c.-18C>T
NM_001145266.2:c.-18C>T
NM_018389.5:c.22C>TMANE SELECT
NP_060859.4:p.Arg8Trp
NP_060859.4:p.Arg8Trp
LRG_107t1:c.22C>T
LRG_107:g.6752C>T
LRG_107p1:p.Arg8Trp
NC_000011.9:g.45827374C>T
NM_001145266.1:c.-18C>T
NM_018389.4:c.22C>T

Protein change:

R8W

Molecular consequence:

NM_001145265.2:c.-18C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_018389.5:c.22C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Leukocyte adhesion deficiency type II
Synonyms:: CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIc; CDG IIc; Congenital disorder of glycosylation type 2C; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009953; MedGen: C0398739; Orphanet: 2968; Orphanet: 99843; OMIM: 266265

Recent activity

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UNVERIFIED: Chysis bractescens ribulose-1,5-bisphosphate carboxylase/oxygenase l...
UNVERIFIED: Chysis bractescens ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit-like (rbcL) gene, partial sequence; chloroplast
gi|380749766|gb|JN589977.1|

Nucleotide
cytidine deaminase [Bacteroides fragilis]
cytidine deaminase [Bacteroides fragilis]
gi|492345511|ref|WP_005816623.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003785963	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 11, 2022)	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

SCV003785963

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 11, 2022)

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 Invitae, SCV003785963.2

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

Description

This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 8 of the SLC35C1 protein (p.Arg8Trp). This variant is present in population databases (rs376834333, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with SLC35C1-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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.

#	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: Sep 1, 2024

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