SLC35A1

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

Basic information

Region (hg38): 6:87470623-87512336

Links

ENSG00000164414

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

Phenotypes

GenCC

Source: genCC

SLC35A1-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 (53 variants)
Inborn_genetic_diseases (23 variants)
not_provided (18 variants)
not_specified (10 variants)
SLC35A1-related_disorder (7 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. These statistics are base on transcript: NM_000006416.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	19 clinvar		20
missense	2 clinvar	2 clinvar	37 clinvar	4 clinvar		45
nonsense			1 clinvar			1
start loss						0
frameshift			3 clinvar			3
splice donor/acceptor (+/-2bp)						0
Total	2	2	42	23	0

Highest pathogenic variant AF is 0.0000013681613

Loading clinvar variants...

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
ghis

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