SLC35E1

protein-coding

solute carrier family 35 member E1, the group of Solute carrier family 35

Gene summary

Predicted to enable antiporter activity. Predicted to be involved in transmembrane transport. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_024881.5

Inheritance

—

ClinVar variants

U:51B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.28

Max pathogenic AF

—

Genomic locus

chr19:16,549,831-16,572,415

External References & Databases

Ensembl (ENSG00000127526)

Transcript & Mutation Effects

hg38 • Region Span ~22.6 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 SLC35E1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 53

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024881.5. 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						0
missense			51 clinvar	2 clinvar		53
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	51	2	0	53

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024881.5	RefSeq	NP_079157.3	6	MANE Select
ENST00000595753.6	Ensembl	ENSP00000470652.1	6	MANE Select
ENST00000409648.8	Ensembl	ENSP00000387152.4	4	Standard
ENST00000421082.1	Ensembl	ENSP00000394092.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

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: ENST00000595753
Coding exons: 6
Length: 22552
Individuals with no LoFs: 125736
Homozygous LoFs: 0
Heterozygous LoFs: 12
Defined: 125748
p: 0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.48	165	228	0.724	0.0000140	2623
Missense (PolyPhen)		33	76.224	0.43293		932
Synonymous	0.532	99	106	0.934	0.00000730	884
Loss of Function	2.49	4	14.1	0.285	6.84e-7	156

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000088	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.124

Intolerance Scores

LoFtool: 0.0999
RVIS EVS: -0.63
RVIS percentile EVS: 17.03

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.470

Gene Damage Prediction

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