Is ENG p.Ala159Asp (c.476C>A) pathogenic?

ENG p.Ala159Asp (c.476C>A) is classified Uncertain significance in ENG (ClinVar, Single submitter, 1 submitter; last evaluated 2021-01-25). AlphaMissense: likely pathogenic (0.5915); Absent from gnomAD v4.1.

How common is ENG p.Ala159Asp (c.476C>A) in the general population?

ENG p.Ala159Asp (c.476C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ENG p.Ala159Asp (c.476C>A)?

AlphaMissense predicts likely pathogenic (score 0.5915) — an in-silico prediction, not a clinical call.

ENG p.Ala159Asp

c.476C>A · VCV4904634

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.5915 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.5915	likely pathogenic
REVEL	0.152	moderately benign-leaning
SaProt	LLR -11.10	damaging
⇒ AlphaMissense and SaProt call this damaging; REVEL does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.17	GERP -4.1
Regional constraint	o/e 0.86	unconstrained · MANE · 39 kb · p 5.2e-05 · regional, not allelic
Overall
CADD	4.79	PHRED · no single calibrated threshold — expert panels disagree

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: ENG
Protein: p.Ala159Asp
Coding: c.476C>A
MANE Select: NM_001114753
Type: single nucleotide variant
Location: chr9:127826557 (GRCh38)
Gene constraint: LOEUF 0.374 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 80.84 · 3 PDB
Residue 159: a β-strand; the 'required for interaction with gdf2' region; the 'or2' region

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

Similar variants

ENG p.Ala159Pro Uncertain significance ★ ⚠ same residue
ENG p.Ala159Ser Uncertain significance ★ ⚠ same residue
ENG p.Arg529His Pathogenic ★★★ same type
ENG p.Asn423Ser Likely pathogenic ★★★ ⚠ same type
ENG p.Cys382Tyr Pathogenic ★★★ same type
ENG p.Cys549Gly Likely pathogenic ★★★ same type
ENG p.Gly331Ser Pathogenic ★★★ ⚠ same type
ENG p.Gly603Arg Likely pathogenic ★★★ 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/eng-p-ala159asp (accessed [today's date]).

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