SLC35E3

protein-coding

solute carrier family 35 member E3, the group of Solute carrier family 35

Gene summary

Predicted to enable antiporter activity and nucleotide-sugar transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be located in membrane. Predicted to be active in Golgi apparatus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_018656.5

Inheritance

—

ClinVar variants

U:40B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.8

Max pathogenic AF

—

Genomic locus

chr12:68,746,125-68,793,964

External References & Databases

Ensembl (ENSG00000175782)

Transcript & Mutation Effects

hg38 • Region Span ~47.8 kb

Loading mutation effect viewer...

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 SLC35E3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 38

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018656.5. 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			37 clinvar	2 clinvar		39
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	40	2	0	42

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018656.5	RefSeq	NP_061126.2	5	MANE Select
ENST00000398004.4	Ensembl	ENSP00000381089.2	5	MANE Select
NM_001354997.3	RefSeq	NP_001341926.1	4	Standard
NM_001354998.2	RefSeq	NP_001341927.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

nucleotide-sugar transmembrane transporter activity
antiporter activity
transmembrane transporter activity

Cellular Component

Golgi apparatus
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000398004
Coding exons: 5
Length: 47623
Individuals with no LoFs: 124701
Homozygous LoFs: 0
Heterozygous LoFs: 94
Defined: 124795
p: 0.000377

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.124	163	168	0.973	0.00000790	2012
Missense (PolyPhen)		26	28.869	0.90061		339
Synonymous	-0.456	73	68.2	1.07	0.00000325	646
Loss of Function	0.706	11	13.8	0.795	6.89e-7	159

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00039	0.00039	rare
Latino/Admixed American	0.00013	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.0020	0.0020	notable
European (Non-Finnish)	0.00031	0.00030	rare
South Asian	0.000033	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Putative transporter. {ECO:0000250}.;

Recessive Scores

pRec: 0.102

Intolerance Scores

LoFtool: 0.705
RVIS EVS: -0.23
RVIS percentile EVS: 37.11

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.182

Gene Damage Prediction

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