NM_018389.5(SLC35C1):c.482T>C (p.Leu161Pro) AND Leukocyte adhesion deficiency type II

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 13, 2019
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:: RCV001216139.1

Allele description

NM_018389.5(SLC35C1):c.482T>C (p.Leu161Pro)

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.482T>C (p.Leu161Pro)

HGVS:

NC_000011.10:g.45806283T>C
NG_009875.1:g.7212T>C
NM_001145265.2:c.443T>C
NM_001145266.2:c.443T>C
NM_018389.5:c.482T>CMANE SELECT
NP_001138737.1:p.Leu148Pro
NP_001138738.1:p.Leu148Pro
NP_001138738.1:p.Leu148Pro
NP_060859.4:p.Leu161Pro
NP_060859.4:p.Leu161Pro
LRG_107t1:c.482T>C
LRG_107:g.7212T>C
LRG_107p1:p.Leu161Pro
NC_000011.9:g.45827834T>C
NM_001145266.1:c.443T>C
NM_018389.4:c.482T>C

Protein change:

L148P

Links:

dbSNP: rs778718913

NCBI 1000 Genomes Browser:

rs778718913

Molecular consequence:

NM_001145265.2:c.443T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001145266.2:c.443T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_018389.5:c.482T>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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Tssr116232 AND (alive[prop]) (0)
Gene
SsrA-binding protein [Arabidopsis thaliana]
SsrA-binding protein [Arabidopsis thaliana]
gi|15221150|ref|NP_175267.1|

Protein
D012101 (1)
MeSH
Reproductive and Urinary Physiological Phenomena
Reproductive and Urinary Physiological Phenomena
Physiology of the human and animal body, male or female, in the processes and characteristics of REPRODUCTION and the URINARY TRACT.<br/>Year introduced: 2009 (1998)

MeSH
ACSBG1 [Meleagris gallopavo]
ACSBG1 [Meleagris gallopavo]
Gene ID:100551321

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001387916	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 13, 2019)	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

SCV001387916

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 13, 2019)

germline

clinical testing

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

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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, SCV001387916.1

#	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 leucine with proline at codon 161 of the SLC35C1 protein (p.Leu161Pro). The leucine residue is moderately conserved and there is a moderate physicochemical difference between leucine and proline. This variant is present in population databases (rs778718913, ExAC 0.006%). This variant has not been reported in the literature in individuals 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: "Possibly Damaging"; Align-GVGD: "Class C15"). 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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