SLC35C1

solute carrier family 35 member C1, the group of Solute carrier family 35

Basic information

Region (hg38): 11:45804071-45813016

Links

ENSG00000181830 ∙ NCBI:55343 ∙ OMIM:605881 ∙ HGNC:20197 ∙ Uniprot:Q96A29 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• leukocyte adhesion deficiency type II (Definitive), mode of inheritance: AR
• leukocyte adhesion deficiency type II (Supportive), mode of inheritance: AR
• leukocyte adhesion deficiency type II (Strong), mode of inheritance: AR
• leukocyte adhesion deficiency type II (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Congenital disorder of glycosylation, type IIc	AR	Allergy/Immunology/Infectious; Biochemical; Hematologic	Treatment with fucose has been described as effective in some individuals; Surveillance for and prompt treatment of infections may be beneficial; Awareness of coagulopathies may be beneficial in terms of medical management, especially in situations such as surgery	Allergy/Immunology/Infectious; Biochemical; Neurologic	1279426; 10590041; 11213799; 11326280; 11133780; 12116250; 21175687; 20301507
Hepatic-metabolized agents should be avoided

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC35C1 gene.

• Leukocyte adhesion deficiency type II (256 variants)
• not provided (27 variants)
• Inborn genetic diseases (14 variants)
• not specified (11 variants)
• Congenital disorder of glycosylation (2 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC35C1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			4	70		74
missense	1	2	105	2	1	111
nonsense	1	2				3
start loss			2			2
frameshift	1		2			3
inframe indel			2			2
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			38	10	19	67
Total	3	4	153	82	20

Highest pathogenic variant AF is 0.0000131

Variants in SLC35C1

This is a list of pathogenic ClinVar variants found in the SLC35C1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-45804190-A-T			Likely benign (Jul 02, 2019)
11-45804395-G-A			Benign (Jun 23, 2018)
11-45805010-A-G			Benign (Jun 23, 2018)
11-45805124-A-G		Leukocyte adhesion deficiency type II	Uncertain significance (Jan 13, 2018)
11-45805137-C-T		Leukocyte adhesion deficiency type II	Likely benign (Jan 13, 2018)
11-45805145-C-A		Leukocyte adhesion deficiency type II	Uncertain significance (Jan 12, 2018)
11-45805149-C-T		Leukocyte adhesion deficiency type II	Uncertain significance (Jan 12, 2018)
11-45805169-T-G		Leukocyte adhesion deficiency type II	Uncertain significance (Jan 13, 2018)
11-45805170-G-A		Leukocyte adhesion deficiency type II	Benign (Jun 23, 2018)
11-45805187-G-C		Leukocyte adhesion deficiency type II	Uncertain significance (Jan 13, 2018)
11-45805233-C-T		Leukocyte adhesion deficiency type II	Uncertain significance (Jan 13, 2018)
11-45805249-A-AAGCCCCG		Congenital disorder of glycosylation	Uncertain significance (Jun 14, 2016)
11-45805284-C-A		Leukocyte adhesion deficiency type II	Uncertain significance (Jan 13, 2018)
11-45805321-G-A		Leukocyte adhesion deficiency type II	Uncertain significance (Jan 12, 2018)
11-45805409-C-T		Leukocyte adhesion deficiency type II	Uncertain significance (Jan 13, 2018)
11-45805490-T-C		Leukocyte adhesion deficiency type II	Uncertain significance (Jan 12, 2018)
11-45805499-G-C		Leukocyte adhesion deficiency type II	Benign (Jun 29, 2018)
11-45805515-C-G		Leukocyte adhesion deficiency type II	Uncertain significance (Apr 27, 2017)
11-45805568-T-G		Leukocyte adhesion deficiency type II	Uncertain significance (Jan 13, 2018)
11-45805584-G-C		Leukocyte adhesion deficiency type II	Uncertain significance (Jan 13, 2018)
11-45805629-C-T		Leukocyte adhesion deficiency type II	Benign (Jan 13, 2018)
11-45805714-T-G		Leukocyte adhesion deficiency type II	Uncertain significance (Jan 13, 2018)
11-45805799-A-G		not specified • Leukocyte adhesion deficiency type II	Benign (Jul 15, 2021)
11-45805811-G-A		Leukocyte adhesion deficiency type II	Uncertain significance (Aug 09, 2022)
11-45805813-C-T		Leukocyte adhesion deficiency type II	Likely benign (Apr 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC35C1	protein_coding	protein_coding	ENST00000314134	2	8944

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0235	0.920	125694	0	6	125700	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	172	221	0.780	0.0000149	2320
Missense in Polyphen		29	60.833	0.47672		663
Synonymous	-1.10	126	111	1.13	0.00000880	802
Loss of Function	1.63	4	9.39	0.426	4.08e-7	99

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in GDP-fucose import from the cytoplasm into the Golgi lumen.
• Disease: DISEASE: Congenital disorder of glycosylation 2C (CDG2C) [MIM:266265]: A multisystem disorder caused by a defect in glycoprotein biosynthesis and characterized by under-glycosylated serum glycoproteins. Congenital disorders of glycosylation result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. The broad spectrum of features reflects the critical role of N- glycoproteins during embryonic development, differentiation, and maintenance of cell functions. The clinical features of CDG2C include mental retardation, short stature, facial stigmata, and recurrent bacterial peripheral infections with persistently elevated peripheral leukocytes. Biochemically, CDG2C is characterized by a lack of fucosylated glycoconjugates, including selectin ligands. {ECO:0000269|PubMed:11326279, ECO:0000269|PubMed:11326280}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Post-translational protein modification;Metabolism of proteins;Purine metabolism;Transport of vitamins, nucleosides, and related molecules;SLC-mediated transmembrane transport;Transport of small molecules;GDP-fucose biosynthesis;Synthesis of substrates in N-glycan biosythesis;Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein;Asparagine N-linked glycosylation;Transport of nucleotide sugars (Consensus)

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.309
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.51

Haploinsufficiency Scores

• pHI: 0.129
• hipred: N
• hipred_score: 0.429
• ghis: 0.442

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.138

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Slc35c1
• Phenotype: hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; immune system phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: carbohydrate transport;lipid glycosylation;protein O-linked fucosylation;GDP-fucose import into Golgi lumen;negative regulation of Notch signaling pathway
• Cellular component: Golgi membrane;Golgi apparatus;integral component of membrane
• Molecular function: GDP-fucose transmembrane transporter activity;antiporter activity;transmembrane transporter activity