Is ENO2 p.Asp142= (c.426C>T) pathogenic?

ENO2 p.Asp142= (c.426C>T) is classified Likely benign in ENO2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-06-06). Rare (popmax 0.188%, sas); Associated with ENO2-related disorder.

What condition is associated with ENO2 p.Asp142= (c.426C>T)?

ENO2 p.Asp142= (c.426C>T) is associated with ENO2-related disorder (ClinVar).

How common is ENO2 p.Asp142= (c.426C>T) in the general population?

ENO2 p.Asp142= (c.426C>T) is rare (popmax 0.188%, sas) (gnomAD).

ENO2 p.Asp142=

c.426C>T · rs782318226 · VCV3043972

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.188%, sas)

Conditions

ENO2-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.7	GERP 1, phastCons 1
Overall
CADD	13.26	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.188% South Asian · 171/90,862 alleles

Filtering AF 0.165% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.156%

Overall 0.0114% 184/1,609,562 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.188%	531
Remaining individualsnot grpmax-eligible	0.0192%	5,198
European (non-Finnish)	8.48e-05%	1,179,162

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: ENO2
Protein: p.Asp142=
Coding: c.426C>T
MANE Select: NM_001975
dbSNP: rs782318226
Type: single nucleotide variant
Location: chr12:6917696 (GRCh38)
Gene constraint: LOEUF 0.542 · pLI 0.84 (gnomAD)
Structure: AlphaFold pLDDT 97.14 · 16 PDB

Full ENO2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ENO2-related disorder

Similar variants

ENO2 p.Leu137= Likely benign same condition
ENO2 p.Ala27Asp Uncertain significance ★ ⚠ same type
ENO2 p.Ala331Thr Uncertain significance ★ ⚠ same type
ENO2 p.Arg126Trp Uncertain significance ★ ⚠ same type
ENO2 p.Arg179Gln Uncertain significance ★ ⚠ same type
ENO2 p.Arg183Gln Uncertain significance ★ ⚠ same type
ENO2 p.Arg269Gln Uncertain significance ★ ⚠ same type
ENO2 p.Arg269Leu 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/eno2-p-asp142 (accessed [today's date]).

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