SLC35C2

solute carrier family 35 member C2, the group of Solute carrier family 35

Basic information

Region (hg38): 20:46345980-46364458

Previous symbols: [ "C20orf5", "OVCOV1" ]

Links

ENSG00000080189 ∙ NCBI:51006 ∙ OMIM:619530 ∙ HGNC:17117 ∙ Uniprot:Q9NQQ7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC35C2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC35C2 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				1		1
missense			30	1		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	2	0

Variants in SLC35C2

This is a list of pathogenic ClinVar variants found in the SLC35C2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-46350435-T-C		not specified	Uncertain significance (Jan 02, 2024)
20-46350449-C-T		not specified	Likely benign (Sep 30, 2024)
20-46350456-T-G		not specified	Uncertain significance (Jan 23, 2023)
20-46350788-C-T		not specified	Uncertain significance (Oct 07, 2024)
20-46350791-G-A		not specified	Uncertain significance (Nov 13, 2024)
20-46350811-C-A		not specified	Uncertain significance (Jan 08, 2024)
20-46350819-G-A			Likely benign (Nov 01, 2022)
20-46350830-A-T		not specified	Uncertain significance (Jun 13, 2023)
20-46350851-C-T		not specified	Uncertain significance (Sep 04, 2024)
20-46350857-G-C		not specified	Uncertain significance (Feb 22, 2023)
20-46352190-A-C		not specified	Uncertain significance (Jun 11, 2024)
20-46352193-C-T		not specified	Uncertain significance (Dec 14, 2023)
20-46352200-T-C		not specified	Uncertain significance (Jan 05, 2022)
20-46352202-T-A		not specified	Uncertain significance (Sep 10, 2024)
20-46354948-C-T		not specified	Uncertain significance (Mar 26, 2024)
20-46354950-A-G		not specified	Uncertain significance (Feb 22, 2023)
20-46354959-T-C		not specified	Uncertain significance (Feb 13, 2024)
20-46355097-T-G		not specified	Uncertain significance (Dec 18, 2023)
20-46355205-C-G		not specified	Uncertain significance (Sep 27, 2024)
20-46355226-G-C		not specified	Uncertain significance (Sep 14, 2022)
20-46355237-G-A		not specified	Uncertain significance (Sep 24, 2024)
20-46355821-A-G		not specified	Uncertain significance (Nov 17, 2022)
20-46356625-G-A		not specified	Uncertain significance (Nov 13, 2024)
20-46357647-A-G		not specified	Uncertain significance (Dec 19, 2023)
20-46357665-C-A		not specified	Uncertain significance (Sep 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC35C2	protein_coding	protein_coding	ENST00000372227	9	14877

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00147	0.970	125685	0	63	125748	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.23	169	220	0.767	0.0000132	2351
Missense in Polyphen		33	56.389	0.58522		644
Synonymous	-0.837	113	102	1.11	0.00000663	780
Loss of Function	1.92	7	15.1	0.465	6.40e-7	175

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000363	0.000362
Ashkenazi Jewish	0.00	0.00
East Asian	0.000574	0.000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000326	0.000325
Middle Eastern	0.000574	0.000544
South Asian	0.000199	0.000196
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play an important role in the cellular response to tissue hypoxia. May be either a GDP-fucose transporter that competes with SLC35C1 for GDP-fucose, or a factor that otherwise enhances the fucosylation of Notch and is required for optimal Notch signaling in mammalian cells. {ECO:0000269|PubMed:20837470}.

Recessive Scores

• pRec: 0.0986

Intolerance Scores

• loftool: 0.242
• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.16

Haploinsufficiency Scores

• pHI: 0.118
• hipred: N
• hipred_score: 0.390
• ghis: 0.557

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.508

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc35c2

Gene ontology

• Biological process: negative regulation of gene expression;UDP-glucose transmembrane transport;protein O-linked fucosylation;positive regulation of Notch signaling pathway
• Cellular component: nucleoplasm;endoplasmic reticulum-Golgi intermediate compartment;Golgi apparatus;cis-Golgi network;integral component of membrane;endoplasmic reticulum-Golgi intermediate compartment membrane
• Molecular function: antiporter activity;transmembrane transporter activity