Is ADH4 p.Pro32His (c.95C>A) pathogenic?

ADH4 p.Pro32His (c.95C>A) is classified Uncertain significance in ADH4 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-05). AlphaMissense: likely pathogenic (0.9705); Ultra-rare (popmax 0.0209%, amr).

How common is ADH4 p.Pro32His (c.95C>A) in the general population?

ADH4 p.Pro32His (c.95C>A) is ultra-rare (popmax 0.0209%, amr) (gnomAD).

What do computational predictors say about ADH4 p.Pro32His (c.95C>A)?

AlphaMissense predicts likely pathogenic (score 0.9705) — an in-silico prediction, not a clinical call.

ADH4 p.Pro32His

c.95C>A · VCV3838160

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9705 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0209%, amr)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.9705	likely pathogenic · top 3% in ADH4
REVEL	0.328	indeterminate
SaProt	LLR -13.49	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.6	GERP 1.8, phastCons 1
Regional constraint	o/e 1.04	unconstrained · MANE · 20 kb · p 0.41 · regional, not allelic
Overall
CADD	22.6	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0209% Admixed American · 12/57,290 alleles

Filtering AF 0.012% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00937%

Overall 0.00694% 111/1,600,558 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0209%	4,774
East Asian	0.0203%	4,937
Remaining individualsnot grpmax-eligible	0.013%	7,706
European (non-Finnish)	0.00655%	15,262
South Asian	0.0045%	22,214
Finnishnot grpmax-eligible	0.00157%	63,800

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: ADH4
Protein: p.Pro32His
Coding: c.95C>A
MANE Select: NM_000670
Type: single nucleotide variant
Location: chr4:99142704 (GRCh38)
Gene constraint: LOEUF 1.077 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 98.23 · 1 PDB
Residue 32: an α-helix

Full ADH4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ADH4 p.Pro32Ala Uncertain significance ★ ⚠ same residue
ADH4 p.Pro32Arg Uncertain significance ★ ⚠ same residue
ADH4 p.Pro32Leu Uncertain significance ★ ⚠ same residue
ADH4 p.Pro32Thr Uncertain significance ★ ⚠ same residue
ADH4 p.Ala15Thr Uncertain significance ★ ⚠ same type
ADH4 p.Ala188Val Uncertain significance ★ ⚠ same type
ADH4 p.Ala222Thr Uncertain significance ★ ⚠ same type
ADH4 p.Ala290Thr 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/adh4-p-pro32his (accessed [today's date]).

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