SLC35A1

solute carrier family 35 member A1, the group of Solute carrier family 35

Basic information

Region (hg38): 6:87470622-87512336

Links

ENSG00000164414 ∙ NCBI:10559 ∙ OMIM:605634 ∙ HGNC:11021 ∙ Uniprot:P78382 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• SRD5A3-congenital disorder of glycosylation (Strong), mode of inheritance: AR
• SLC35A1-congenital disorder of glycosylation (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Congenital disorder of glycosylation, type IIf	AR	Allergy/Immunology/Infectious; Hematologic	The condition can include infectious risks (as well as other hematologic anomalies), and antiinnfectious prophylaxis and early and aggressive treatment of infections may be beneficial; BMT has been described; Awareness of coagulopathies may be beneficial in terms of medical management, especially in situations such as surgery	Allergy/Immunology/Infectious; Hematologic; Neurologic	11157507; 15576474
Hepatic-metabolized medications should be avoided

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC35A1 gene.

• SLC35A1-congenital disorder of glycosylation (42 variants)
• not provided (32 variants)
• not specified (14 variants)
• Inborn genetic diseases (12 variants)
• Congenital disorder of glycosylation (10 variants)
• Pontoneocerebellar hypoplasia (7 variants)
• - (3 variants)
• CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIf, MODIFIER OF (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC35A1 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				16		16
missense			22	2		24
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region				4	1	5
non coding			4	18	17	39
Total	0	0	29	36	17

Variants in SLC35A1

This is a list of pathogenic ClinVar variants found in the SLC35A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-87472721-T-C			Benign (Jul 27, 2018)
6-87472969-C-T			Likely benign (May 21, 2018)
6-87472981-C-T		not specified	Likely benign (Feb 19, 2018)
6-87472983-G-A		not specified	Likely benign (Oct 18, 2016)
6-87472986-G-C		not specified • SLC35A1-congenital disorder of glycosylation	Benign (Jul 15, 2021)
6-87473010-G-A		SLC35A1-congenital disorder of glycosylation	Uncertain significance (Aug 17, 2023)
6-87473010-G-T		not specified • SLC35A1-congenital disorder of glycosylation	Conflicting classifications of pathogenicity (Jan 22, 2024)
6-87473038-G-A		SLC35A1-congenital disorder of glycosylation	Benign (Nov 23, 2020)
6-87473040-G-T			Benign (Jan 23, 2020)
6-87473325-G-C			Benign (Oct 16, 2018)
6-87477166-G-GGT			Likely benign (Nov 23, 2019)
6-87477166-G-GGTGT			Benign (Nov 23, 2019)
6-87477166-G-GGTGTGTGT			Benign (Jun 04, 2021)
6-87477213-C-T			Benign (Apr 09, 2019)
6-87477214-A-G			Benign (Jun 29, 2018)
6-87477364-A-C		not specified • SLC35A1-congenital disorder of glycosylation • SLC35A1-related disorder	Benign/Likely benign (Jan 22, 2024)
6-87477393-C-T		SLC35A1-congenital disorder of glycosylation	Likely benign (Jan 29, 2019)
6-87477399-A-C			Likely benign (Dec 03, 2018)
6-87477427-A-G		Inborn genetic diseases	Uncertain significance (Dec 28, 2022)
6-87477459-C-T			Likely benign (Jul 05, 2018)
6-87477478-A-G		SLC35A1-congenital disorder of glycosylation • not specified • SLC35A1-related disorder	Conflicting classifications of pathogenicity (Feb 01, 2024)
6-87477486-C-T		SLC35A1-related disorder	Likely benign (Jun 25, 2019)
6-87477487-G-A		Inborn genetic diseases	Uncertain significance (Sep 13, 2023)
6-87477492-T-C		-	no classification for the single variant (-)
6-87477516-G-T		SLC35A1-congenital disorder of glycosylation • Inborn genetic diseases	Uncertain significance (Aug 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC35A1	protein_coding	protein_coding	ENST00000369552	8	41714

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.683	0.317	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.27	122	168	0.724	0.00000804	2115
Missense in Polyphen		16	39.669	0.40334		509
Synonymous	-0.180	70	68.1	1.03	0.00000360	688
Loss of Function	3.12	3	16.8	0.178	7.04e-7	245

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000213
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000792	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transports CMP-sialic acid from the cytosol into Golgi vesicles where glycosyltransferases function.
• Disease: DISEASE: Congenital disorder of glycosylation 2F (CDG2F) [MIM:603585]: CDGs are a family of severe inherited diseases caused by a defect in protein N-glycosylation. They are characterized by under-glycosylated serum proteins. These multisystem disorders present with a wide variety of clinical features, such as disorders of 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. {ECO:0000269|PubMed:15576474}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Post-translational protein modification;Metabolism of proteins;Transport of vitamins, nucleosides, and related molecules;SLC-mediated transmembrane transport;Transport of small molecules;Pyrimidine metabolism;Sialic acid metabolism;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)

Intolerance Scores

• loftool: 0.362
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63

Haploinsufficiency Scores

• pHI: 0.538
• hipred: Y
• hipred_score: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc35a1
• 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)

Gene ontology

• Biological process: carbohydrate metabolic process;cellular protein modification process;carbohydrate transport;sialic acid transport;CMP-N-acetylneuraminate transmembrane transport
• Cellular component: Golgi membrane;Golgi apparatus;integral component of plasma membrane;integral component of Golgi membrane
• Molecular function: CMP-N-acetylneuraminate transmembrane transporter activity;sialic acid transmembrane transporter activity