Is ERLIN2 p.Ala160Asp (c.479C>A) pathogenic?

ERLIN2 p.Ala160Asp (c.479C>A) is classified Uncertain significance in ERLIN2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-16). AlphaMissense: likely pathogenic (0.9943); Absent from gnomAD v4.1.

How common is ERLIN2 p.Ala160Asp (c.479C>A) in the general population?

ERLIN2 p.Ala160Asp (c.479C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ERLIN2 p.Ala160Asp (c.479C>A)?

AlphaMissense predicts likely pathogenic (score 0.9943) — an in-silico prediction, not a clinical call.

ERLIN2 p.Ala160Asp

c.479C>A · VCV3911079

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9943 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9943	likely pathogenic
REVEL	0.928	moderately pathogenic-leaning
SaProt	LLR -14.69	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 2.7, phastCons 1
Regional constraint	o/e 0.60	unconstrained · MANE · 9,452 bp · p 1e-10 · regional, not allelic
Overall
CADD	32.0	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.Ala160Asp
Coding: c.479C>A
MANE Select: NM_007175
Type: single nucleotide variant
Location: chr8:37749613 (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

Similar variants

ERLIN2 p.Ala151Val Pathogenic/Likely pathogenic ★★ same type
ERLIN2 p.Gln63Lys Pathogenic/Likely pathogenic ★★ same type
ERLIN2 p.Val168Met Pathogenic/Likely pathogenic ★★ same type
ERLIN2 c.298+5G>A Uncertain significance ★★ same type
ERLIN2 c.819+3A>G Uncertain significance ★★ same type
ERLIN2 p.Ala288Pro Uncertain significance ★★ ⚠ same type
ERLIN2 p.Ala290Val Uncertain significance ★★ ⚠ same type
ERLIN2 p.Ala99Thr Uncertain significance ★★ ⚠ same type

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-ala160asp (accessed [today's date]).

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