Is ERLIN2 p.Ala17Val (c.50C>T) pathogenic?

ERLIN2 p.Ala17Val (c.50C>T) is classified Uncertain significance in ERLIN2 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-10-14). AlphaMissense: likely benign (0.1124); Absent from gnomAD v4.1.

How common is ERLIN2 p.Ala17Val (c.50C>T) in the general population?

ERLIN2 p.Ala17Val (c.50C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ERLIN2 p.Ala17Val (c.50C>T)?

AlphaMissense predicts likely benign (score 0.1124) — an in-silico prediction, not a clinical call.

ERLIN2 p.Ala17Val

c.50C>T · rs2129641485 · VCV1313297

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1124 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1124	likely benign
REVEL	0.171	moderately benign-leaning
SaProt	LLR -5.36	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 2.8, phastCons 1
Regional constraint	o/e 0.67	unconstrained · MANE · 6,689 bp · p 9.5e-05 · regional, not allelic
Overall
CADD	25.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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.Ala17Val
Coding: c.50C>T
MANE Select: NM_007175
dbSNP: rs2129641485
Type: single nucleotide variant
Location: chr8:37737972 (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-ala17val (accessed [today's date]).

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