Is ETHE1 p.Phe142= (c.426C>T) pathogenic?

ETHE1 p.Phe142= (c.426C>T) is classified Likely benign in ETHE1 (ClinVar, Single submitter, 2 submitters; last evaluated 2026-01-26). Rare (popmax 0.11%, sas); Associated with ethylmalonic encephalopathy.

What condition is associated with ETHE1 p.Phe142= (c.426C>T)?

ETHE1 p.Phe142= (c.426C>T) is associated with ethylmalonic encephalopathy (ClinVar).

How common is ETHE1 p.Phe142= (c.426C>T) in the general population?

ETHE1 p.Phe142= (c.426C>T) is rare (popmax 0.11%, sas) (gnomAD).

How is Ethylmalonic encephalopathy inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

ETHE1 p.Phe142=

c.426C>T · rs566533497 · VCV754192

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.11%, sas)

Conditions

ethylmalonic encephalopathy

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 -0.077	GERP -5.3, phastCons 0.06
Overall
CADD	8.572	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.11% South Asian · 100/91,082 alleles

Filtering AF 0.0923% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0858%

Overall 0.01% 162/1,614,172 alleles · rare exomes 154/1,461,856 · genomes 8/152,316 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.11%	911
Middle Eastern	0.066%	1,516
Remaining individualsnot grpmax-eligible	0.0224%	4,465
Admixed American	0.0117%	8,574
East Asian	0.00669%	14,959
European (non-Finnish)	0.00271%	36,876
African / African-American	0.00266%	37,528

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: ETHE1
Protein: p.Phe142=
Coding: c.426C>T
MANE Select: NM_014297
dbSNP: rs566533497
Type: single nucleotide variant
Location: chr19:43511516 (GRCh38)
Gene constraint: LOEUF 0.97 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.05 · 1 PDB
Residue 142: a β-strand

Full ETHE1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ethylmalonic encephalopathy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Ethylmalonic encephalopathy (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

ETHE1 c.505+1G>A Pathogenic ★★★ same condition
ETHE1 c.505+1G>T Pathogenic ★★★ same condition
ETHE1 p.Arg163Gln Pathogenic ★★★ same condition
ETHE1 p.Arg163Trp Pathogenic ★★★ same condition
ETHE1 p.Ala254Val Uncertain significance ★★★ ⚠ same condition
ETHE1 p.Arg124Leu Uncertain significance ★★★ ⚠ same condition
ETHE1 p.Lys66Arg Uncertain significance ★★★ ⚠ same condition
ETHE1 p.Val143Ile 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/ethe1-p-phe142 (accessed [today's date]).

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