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Primary immunodeficiency

Gene: SLC35C1

Green List (high evidence)

SLC35C1 (solute carrier family 35 member C1)
EnsemblGeneIds (GRCh38): ENSG00000181830
EnsemblGeneIds (GRCh37): ENSG00000181830
OMIM: 605881, Gene2Phenotype
SLC35C1 is in 11 panels

5 reviews

Kimberly Gilmour (Great Ormond Street Hopsital)

Green List (high evidence)

agree with green gene
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94

Tracy Briggs (Manchester Genomic Medicine Centre)

Green List (high evidence)

YES- this is covered on our targeted exome
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94

Sophie Hambleton (Newcastle University)

Green List (high evidence)

Eleanor Williams (Genomics England Curator)

Green List (high evidence)

Comment on list classification: Rating this gene green since likely pathogenic variants found in 3 independant families
Created: 15 May 2018, 4:22 p.m.
SLC35C1 is associated with Congenital disorder of glycosylation type IIc (CDG2C) in OMIM. OMIM states it is also known as leukocyte adhesion deficiency II and is characterised by a lack of fucosylated glycoconjugates causing immunodeficiency and severe mental and growth retardation so this phenotype is relevant to the PID panel. Lühn et al., 2001 (PMID:11326279) identified a homozygous mutation (R147C) in the SLC35C1 gene from fibroblasts of a Turkish patient with CDG2C (R147C). This was confirmed by Lubke et al., 2001 (PMID: 11326280). Lubke et al., 2001 also identified another homozygous mutation (T308R) in the SLC35C1 gene in 2 additional patients with LAD2 from unrelated Arab families in Israel. These two substitutions are located in highly conserved transmembrane domains Etzioni et al. 2002 (PMID: 12116250) reported that the previously reported variants in Arab-Israeli families (Lubke et al., 2001, Etzioni et al., 1992 (PMID: 1279426 and Etzioni and Tonetti, 2000 (PMID: 11213799) were homozygous for the T308R mutation. All 3 patients lived in the same area, suggesting a founder mutation. Dauber et al. (2014) (PMID:24403049) report 2 British brothers with congenital disorder of glycosylation type IIc (CDG2C; 266265), Dauber et al. (2014) identified compound heterozygous mutations in the SLC35C1 gene: a E31X substitution, and a 3-bp deletion c.501_503delCTT resulting in the loss of a phenylalanine in the fifth transmembrane domain. The mutations segregated with the disorder in the family. Gene2Phenotype list 3 variants (one nonsense, two missense) in this gene associated with Congenital disorder of glycosylation. Rating this gene green since likely pathogenic variants found in 3 independant families (Lühn et al. 2001, Lubke et al., 2001/Etzioni et al. 2002 and Dauber et al. 2014).
Created: 15 May 2018, 4:22 p.m.
Comment on phenotypes: Added MIM number to Congenital disorder of glycosylation, type IIc
Created: 10 May 2018, 2:41 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Publications

Louise Daugherty (Genomics England Curator)

Green List (high evidence)

Gene rating submitted by Kimberly Gilmour and Austen Worth on behalf of London North GLH for the GMS Immunology specialist test group. As discussed with the GMS Immunology Specialist Test Group during webex call 28th March 2019 and confirmed in follow up email 6th September the Specialist Test Group all agreed there is enough evidence to rate this gene Green.
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
Gene rating submitted by Tracy Briggs, David Gokhale and Abigal Rousseau on behalf of North West GLH for the GMS Immunology specialist test group. As discussed with the GMS Immunology Specialist Test Group during webex call 28th March 2019 and confirmed in follow up email on 20th June the Specialist Test Group all agreed there is enough evidence to rate this gene Green.
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): SLC35C1 .PanelApp HGNC gene symbol check: SLC35C1 . IUIS Disease: Leukocyte adhesion deficiency type 2 (LAD2) . IUIS Inheritance: AR .T cells: Increased activated T cells, .B cells: N/A, .IUIS Other affected cells: N + M. IUIS Associated features: Mild LAD type 1 features with hh-blood group, growth retardation, developmental delay. IUIS Major category: Congenital defects of phagocyte number or function. IUIS Subcategory: Defects of Motility
Created: 2 Jul 2018, 10:35 a.m.
This gene was absent from the original PanelApp PID panel dataset (review April 2018). However it was listed in external expert immunodeficiency diagnostic gene list(s)
GOSH or GRID. In this combined PID panel, this gene has been rated as AMBER and needs further curational review to assess pertinence prior to v1.
Created: 19 Apr 2018, 3:09 p.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: LAD2 / FUCT1, PanelApp HGNC gene symbol check: SLC35C1, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Phagocytic disorders / Leukocyte adhesion deficiency (LAD) / Leukocyte adhesion deficiency (LAD)
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: SLC35C1, GRID_Gene_Symbol: SLC35C1, GRID_Transcript_ENS_Community submitted: ENST00000314134, GRID_Transcript_RefSeq: NM_018389.4, GRID_Transcript_ENS_used_on_Production: ENST00000314134
Created: 17 Apr 2018, 12:12 p.m.

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • NHS GMS
  • North West GLH
  • London North GLH
  • IUIS Classification February 2018
  • Victorian Clinical Genetics Services
  • Expert Review Green
  • ESID Registry 20171117
  • GRID V2.0
Phenotypes
  • Congenital disorder of glycosylation, type IIc 266265
  • Leukocyte adhesion deficiency (LAD)
  • Mild LAD type 1 features with hh-blood group, growth retardation, developmental delay
  • Congenital defects of phagocyte number or function
OMIM
605881
Clinvar variants
Variants in SLC35C1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source NHS GMS was added to SLC35C1.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to SLC35C1.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to SLC35C1.

12 Jul 2018, Gel status: 4

Panel promoted to version 1.0

Louise Daugherty (Genomics England Curator)

2018-07-12 Louise Daugherty (Genomics England Curator) promoted panel to v1.0. Reviews were assessed, and panel was revised according to expert reviews and further in-house curation based on PanelApp guidelines. Previous panels (A- or hypo-gammaglobulinaemia, Congenital neutropaenia, Agranulocytosis, Combined B and T cell defect, Inherited complement deficiency and SCID panels) that were merged with this panel, were checked again for any changes/new reviews prior to versioning of this panel, these merged panels are now retired/made internal.

1 Jul 2018, Gel status: 4

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene SLC35C1 were set to Congenital disorder of glycosylation, type IIc 266265, Leukocyte adhesion deficiency (LAD), Mild LAD type 1 features with hh-blood group, growth retardation, developmental delay, Congenital defects of phagocyte number or function

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to SLC35C1. Panel: Primary immunodeficiency disorders

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

Victorian Clinical Genetics Services was added to SLC35C1. Panel: Primary immunodeficiency disorders

13 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: slc35c1 has been classified as Green List (High Evidence).

13 Jun 2018, Gel status: 3

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: SLC35C1 were set to 11326279; 11326280; 12116250; 1279426; 11213799; 24403049

15 May 2018, Gel status: 3

Gene classified by Genomics England curator

Eleanor Williams (Genomics England Curator)

This gene has been classified as Green List (High Evidence).

10 May 2018, Gel status: 2

Set Phenotypes

Eleanor Williams (Genomics England Curator)

Phenotypes for SLC35C1 were set to Congenital disorder of glycosylation, type IIc 266265; Leukocyte adhesion deficiency (LAD)

19 Apr 2018, Gel status: 2

Gene classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

This gene has been classified as Amber List (Moderate Evidence).

17 Apr 2018, Gel status: 1

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

ESID Registry 20171117 was added to SLC35C1. Panel: Primary immunodeficiency disorders Phenotypes for gene SLC35C1 were set to Congenital disorder of glycosylation, type IIc, Leukocyte adhesion deficiency (LAD)

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene SLC35C1 were set to Congenital disorder of glycosylation, type IIc

17 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

SLC35C1 was added to Primary immunodeficiency disorders panel. Sources: GRID V2.0

17 Apr 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

SLC35C1 was created by Louise Daugherty