RTN2

Chr 19ARAD

reticulon 2

Also known as: HMNR11, NSP2, NSPL1, NSPLI, SPG12

The RTN2 protein localizes to the endoplasmic reticulum where it inhibits amyloid precursor protein processing and enhances trafficking of transporters including glutamate and glucose transporters to the cell surface. Mutations cause either autosomal dominant spastic paraplegia-12 or autosomal recessive distal hereditary motor neuronopathy with spasticity, both affecting motor neurons and causing progressive spasticity. The gene shows moderate constraint against loss-of-function variants (LOEUF 0.417), and the differing inheritance patterns suggest distinct pathogenic mechanisms for different mutation types.

OMIMResearchSummary from RefSeq, OMIM, UniProt
MultiplemechanismAR/ADLOEUF 0.422 OMIM phenotypes
Clinical SummaryRTN2
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.22) despite low pLI — interpret in context.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Moderate LoF intolerance
LoF Constraint
0.42LOEUF
pLI 0.416
Z-score 4.05
OE 0.22 (0.130.42)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
0.70Z-score
OE missense 0.89 (0.810.98)
306 obs / 342.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.22 (0.130.42)
00.351.4
Missense OE0.89 (0.810.98)
00.61.4
Synonymous OE0.93
01.21.6
LoF obs/exp: 7 / 31.5Missense obs/exp: 306 / 342.5Syn Z: 0.72
DN
0.5770th %ile
GOF
0.7029th %ile
LOF
0.4430th %ile

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

GOFprediction above median
LOF1 literature citation · LOEUF 0.42

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.

Literature Evidence

LOFPatient 11 has a heterozygous frameshift variant in RTN2. As two of the three SPG12-causing variants in this gene described to date are null variants, haploinsufficiency of RTN2 seems to cause SPG12.PMID:27165006

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

RTN2 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC