SLC35E2A

Chr 1

solute carrier family 35 member E2A (pseudogene)

Also known as: SLC35E2, SLC35E2AP, SLC35E2P

NCBI Gene: 9906ENSG00000215790UniProt: P0CK97

This gene encodes a putative transporter protein predicted to function as an antiporter in the Golgi apparatus, facilitating transmembrane transport. The gene shows low constraint against loss-of-function variants (pLI 0.0008, LOEUF 1.66), suggesting it may tolerate such variants relatively well. Currently, no specific diseases have been definitively associated with mutations in SLC35E2A.

Summary from RefSeq, UniProt
Research Assistant →
0
Active trials
0
Pubs (1 yr)
140
P/LP submissions
0%
P/LP missense
1.66
LOEUF
Multiple*
Mechanism· predicted
Clinical Summary— SLC35E2A
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
133 unique Pathogenic / Likely Pathogenic· 54 VUS of 195 total submissions
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.66LOEUF
pLI 0.001
Z-score 0.38
OE 0.83 (0.43–1.66)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.18Z-score
OE missense 0.95 (0.82–1.11)
118 obs / 123.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.83 (0.43–1.66)
0≤0.351.4
Missense OE0.95 (0.82–1.11)
0≤0.61.4
Synonymous OE1.17
0≤1.21.6
LoF obs/exp: 5 / 6.0Missense obs/exp: 118 / 123.7Syn Z: -0.93
DN
0.74top 25%
GOF
0.73top 25%
LOF
0.3066th %ile

This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

DNprediction above median
GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

195 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic125
Likely Pathogenic8
VUS54
Likely Benign6
125
Pathogenic
8
Likely Pathogenic
54
VUS
6
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
125
0
125
Likely Pathogenic
0
0
8
0
8
VUS
0
0
54
0
54
Likely Benign
0
0
6
0
6
Benign
0
0
0
0
0
Total001930193

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

SLC35E2A · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 1 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

No open access results found

Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients