SLC35B4

protein-coding

solute carrier family 35 member B4, the group of Solute carrier family 35

Gene summary

Glycosyltransferases, such as SLC35B4, transport nucleotide sugars from the cytoplasm where they are synthesized, to the Golgi apparatus where they are utilized in the synthesis of glycoproteins, glycolipids, and proteoglycans (Ashikov et al., 2005 [PubMed 15911612]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_032826.5

Inheritance

—

ClinVar variants

U:43B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.57

Max pathogenic AF

—

Genomic locus

chr7:134,289,332-134,316,930

External References & Databases

Ensembl (ENSG00000205060)

Transcript & Mutation Effects

hg38 • Region Span ~27.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC35B4 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 41

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032826.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			40 clinvar	2 clinvar		42
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	43	3	0	46

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032826.5	RefSeq	NP_116215.1	10	MANE Select
ENST00000378509.9	Ensembl	ENSP00000367770.4	10	MANE Select
ENST00000416907.5	Ensembl	ENSP00000405445.1	5	Standard
ENST00000470969.2	Ensembl	ENSP00000485857.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Proteoglycan biosynthesis
Transport of vitamins, nucleosides, and related molecules
SLC-mediated transmembrane transport
Transport of small molecules
Galactose metabolism

Biological Process

regulation of gluconeogenesis
carbohydrate transport
UDP-xylose transmembrane transport
3'-phospho-5'-adenylyl sulfate transmembrane transport
UDP-N-acetylglucosamine transmembrane transport

Molecular Function

UDP-N-acetylglucosamine transmembrane transporter activity
UDP-xylose transmembrane transporter activity
protein binding
transmembrane transporter activity

Cellular Component

Golgi membrane
endoplasmic reticulum
Golgi apparatus
integral component of Golgi membrane
integral component of endoplasmic reticulum membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000378509
Coding exons: 10
Length: 27720
Individuals with no LoFs: 125702
Homozygous LoFs: 0
Heterozygous LoFs: 45
Defined: 125747
p: 0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.20	140	186	0.752	0.00000967	2179
Missense (PolyPhen)		37	53.004	0.69806		622
Synonymous	-0.320	75	71.6	1.05	0.00000411	628
Loss of Function	1.68	10	17.6	0.567	9.42e-7	200

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00028	0.00026	rare
South Asian	0.00016	0.00016	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Sugar transporter that specifically mediates the transport of UDP-xylose (UDP-Xyl) and UDP-N-acetylglucosamine (UDP-GlcNAc) from cytosol into Golgi. {ECO:0000269|PubMed:15911612}.;

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.586
RVIS EVS: -0.25
RVIS percentile EVS: 35.75

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.593

Gene Damage Prediction

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