NM_018389.5(SLC35C1):c.260T>C (p.Leu87Pro) AND Leukocyte adhesion deficiency type II

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 16, 2021
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:: RCV002037619.6

Allele description [Variation Report for NM_018389.5(SLC35C1):c.260T>C (p.Leu87Pro)]

NM_018389.5(SLC35C1):c.260T>C (p.Leu87Pro)

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.260T>C (p.Leu87Pro)

HGVS:

NC_000011.10:g.45806061T>C
NG_009875.1:g.6990T>C
NM_001145265.2:c.221T>C
NM_001145266.2:c.221T>C
NM_018389.5:c.260T>CMANE SELECT
NP_001138737.1:p.Leu74Pro
NP_001138738.1:p.Leu74Pro
NP_001138738.1:p.Leu74Pro
NP_060859.4:p.Leu87Pro
NP_060859.4:p.Leu87Pro
LRG_107t1:c.260T>C
LRG_107:g.6990T>C
LRG_107p1:p.Leu87Pro
NC_000011.9:g.45827612T>C
NM_001145266.1:c.221T>C
NM_018389.4:c.260T>C

Protein change:

L74P

Links:

dbSNP: rs2134590175

NCBI 1000 Genomes Browser:

rs2134590175

Molecular consequence:

NM_001145265.2:c.221T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001145266.2:c.221T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_018389.5:c.260T>C - 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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bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase protei...
bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase protein [Streptococcus uberis 0140J]
gi|222152431|ref|YP_002561606.1|

Protein
bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase precur...
bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase precursor protein [Streptococcus suis SC84]
gi|253752737|ref|YP_003025878.1|

Protein
LysM domain-containing protein [Verticillium dahliae VdLs.17]
LysM domain-containing protein [Verticillium dahliae VdLs.17]
gi|697081548|ref|XP_009654198.1|

Protein
PREDICTED: Athalia rosae uncharacterized LOC105686730 (LOC105686730), transcript...
PREDICTED: Athalia rosae uncharacterized LOC105686730 (LOC105686730), transcript variant X3, ncRNA
gi|2252054174|ref|XR_007280009.1|

Nucleotide
PREDICTED: Athalia rosae exonuclease mut-7 homolog (LOC105688140), transcript va...
PREDICTED: Athalia rosae exonuclease mut-7 homolog (LOC105688140), transcript variant X1, mRNA
gi|2252054153|ref|XM_048659965.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002108114	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 16, 2021)	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

SCV002108114

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 16, 2021)

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, SCV002108114.3

#	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. 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: "Possibly Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with SLC35C1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces leucine with proline at codon 87 of the SLC35C1 protein (p.Leu87Pro). The leucine residue is moderately conserved and there is a moderate physicochemical difference between leucine and proline.

#	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 29, 2024

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