Is PPARD p.Arg379His (c.1136G>A) pathogenic?

PPARD p.Arg379His (c.1136G>A) is classified Uncertain significance in PPARD (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-17). AlphaMissense: likely benign (0.0756); Very rare (popmax 0.005%, amr).

How common is PPARD p.Arg379His (c.1136G>A) in the general population?

PPARD p.Arg379His (c.1136G>A) is very rare (popmax 0.005%, amr) (gnomAD).

What do computational predictors say about PPARD p.Arg379His (c.1136G>A)?

AlphaMissense predicts likely benign (score 0.0756) — an in-silico prediction, not a clinical call.

PPARD p.Arg379His

c.1136G>A · VCV4570679

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0756 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.005%, amr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.0756	likely benign
REVEL	0.335	indeterminate
SaProt	LLR -6.86	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.6	GERP -3.5, phastCons 1
Regional constraint	o/e 0.67	unconstrained · MANE · 15 kb · p 2.9e-16 · regional, not allelic
Overall
CADD	23.5	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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 0.005% Admixed American · 3/60,000 alleles

Filtering AF 0.00133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0009%

Overall 0.00149% 24/1,613,958 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.005%	20,000
European (non-Finnish)	0.00169%	59,001
Remaining individualsnot grpmax-eligible	0.0016%	62,484

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: PPARD
Protein: p.Arg379His
Coding: c.1136G>A
MANE Select: NM_006238
Type: single nucleotide variant
Location: chr6:35425889 (GRCh38)
Gene constraint: LOEUF 0.311 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 83.65 · 56 PDB
Residue 379: the nr lbd domain; an α-helix

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

Similar variants

PPARD p.Ala158Val Uncertain significance ★ ⚠ same type
PPARD p.Ala209Val Uncertain significance ★ ⚠ same type
PPARD p.Ala21Pro Uncertain significance ★ ⚠ same type
PPARD p.Ala292Thr Uncertain significance ★ ⚠ same type
PPARD p.Ala392Asp Uncertain significance ★ ⚠ same type
PPARD p.Arg103His Uncertain significance ★ ⚠ same type
PPARD p.Arg113His Uncertain significance ★ ⚠ same type
PPARD p.Arg12Trp 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/ppard-p-arg379his (accessed [today's date]).

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