Is ERLIN2 p.Val136Ile (c.406G>A) pathogenic?

ERLIN2 p.Val136Ile (c.406G>A) is classified Uncertain significance in ERLIN2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-01). AlphaMissense: likely pathogenic (0.6608); Absent from gnomAD v4.1; Associated with Spastic paraplegia.

What condition is associated with ERLIN2 p.Val136Ile (c.406G>A)?

ERLIN2 p.Val136Ile (c.406G>A) is associated with Spastic paraplegia, hereditary spastic paraplegia (ClinVar).

How common is ERLIN2 p.Val136Ile (c.406G>A) in the general population?

ERLIN2 p.Val136Ile (c.406G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ERLIN2 p.Val136Ile (c.406G>A)?

AlphaMissense predicts likely pathogenic (score 0.6608) — an in-silico prediction, not a clinical call.

ERLIN2 p.Val136Ile

c.406G>A · rs1338086200 · VCV528006

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely pathogenic

0.6608 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Spastic paraplegia

Computational evidence

Protein change
AlphaMissense	0.6608	likely pathogenic
REVEL	0.588	indeterminate
SaProt	LLR -10.21	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.8, phastCons 1
Regional constraint	o/e 0.60	unconstrained · MANE · 9,452 bp · p 1e-10 · regional, not allelic
Overall
CADD	31.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: ERLIN2
Protein: p.Val136Ile
Coding: c.406G>A
MANE Select: NM_007175
dbSNP: rs1338086200
Type: single nucleotide variant
Location: chr8:37744678 (GRCh38)
Gene constraint: LOEUF 0.703 · pLI 0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.35 · 5 PDB

Full ERLIN2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Spastic paraplegia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hereditary spastic paraplegia

Similar variants

ERLIN2 p.Val136Leu Uncertain significance ★ ⚠ same residue
ERLIN2 p.Val136= Likely benign ★ same residue
ERLIN2 p.Ala151Val Pathogenic/Likely pathogenic ★★ same condition
ERLIN2 p.Gln63Lys Pathogenic/Likely pathogenic ★★ same condition
ERLIN2 c.298+5G>A Uncertain significance ★★ same condition
ERLIN2 c.819+3A>G Uncertain significance ★★ same condition
ERLIN2 p.Ala290Val Uncertain significance ★★ ⚠ same condition
ERLIN2 p.Ala99Thr Uncertain significance ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/erlin2-p-val136ile (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown