Is EHHADH p.Cys400= (c.1200C>T) pathogenic?

EHHADH p.Cys400= (c.1200C>T) is classified Likely benign in EHHADH (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-05-02). Absent from gnomAD v4.1; Associated with EHHADH-related disorder.

What condition is associated with EHHADH p.Cys400= (c.1200C>T)?

EHHADH p.Cys400= (c.1200C>T) is associated with EHHADH-related disorder (ClinVar).

How common is EHHADH p.Cys400= (c.1200C>T) in the general population?

EHHADH p.Cys400= (c.1200C>T) is absent from gnomAD v4.1 (gnomAD).

EHHADH p.Cys400=

c.1200C>T · rs1426180955 · VCV3047771

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

EHHADH-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 1.3	GERP 1.2, phastCons 1
Overall
CADD	5.555	PHRED · no single calibrated threshold — expert panels disagree

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: EHHADH
Protein: p.Cys400=
Coding: c.1200C>T
MANE Select: NM_001966
dbSNP: rs1426180955
Type: single nucleotide variant
Location: chr3:185193198 (GRCh38)
Gene constraint: LOEUF 0.873 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.07
Residue 400: the '3-hydroxyacyl-coa dehydrogenase' region

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

Disease context

EHHADH-related disorder

Similar variants

EHHADH p.Pro694Leu Uncertain significance ★★ ⚠ same condition
EHHADH p.Glu3Lys Likely pathogenic ★ ⚠ same condition
EHHADH p.Ala550Thr Uncertain significance ★ ⚠ same condition
EHHADH p.His432Tyr Uncertain significance ★ ⚠ same condition
EHHADH p.Pro225Ala Conflicting classifications of pathogenicity ★ ⚠ same condition
EHHADH p.Asp161His Uncertain significance ⚠ same condition
EHHADH p.Asp170Asn Uncertain significance ⚠ same condition
EHHADH p.Gly155Arg Uncertain significance ⚠ same condition

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-cys400 (accessed [today's date]).

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