Is EHHADH p.Pro690del (c.2069_2071del) pathogenic?

EHHADH p.Pro690del (c.20692071del) is classified Uncertain significance in EHHADH (ClinVar, Single submitter, 1 submitter; last evaluated 2017-03-21). Rare (popmax 0.1%, eas).

How common is EHHADH p.Pro690del (c.2069_2071del) in the general population?

EHHADH p.Pro690del (c.2069_2071del) is rare (popmax 0.1%, eas) (gnomAD).

EHHADH p.Pro690del

c.2069_2071del · rs781751204 · VCV500970

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.1%, eas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.8	GERP 2, phastCons 1
Overall
CADD	16.34	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.1% East Asian · 45/44,884 alleles

Filtering AF 0.077% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0688%

Overall 0.00279% 45/1,614,116 alleles · rare

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: EHHADH
Protein: p.Pro690del
Coding: c.2069_2071del
MANE Select: NM_001966
dbSNP: rs781751204
Type: Deletion
Location: chr3:185192327 (GRCh38)
Gene constraint: LOEUF 0.873 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.07

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

Similar variants

EHHADH p.Ala39_Val40insTer Conflicting classifications of pathogenicity ★ same type
EHHADH p.Lys591fs Uncertain significance ★ same type
EHHADH p.Thr27del Uncertain significance ★ same type
EHHADH c.352-21del Likely benign ★ same type
EHHADH c.910+257del Benign ★ same type
EHHADH p.Arg196fs 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/ehhadh-p-pro690del (accessed [today's date]).

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