Is ABCD4 p.Arg579Gln (c.1736G>A) pathogenic?

ABCD4 p.Arg579Gln (c.1736G>A) is classified Benign/Likely benign in ABCD4 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-06-01). AlphaMissense: ambiguous (0.5386); Rare (popmax 0.575%, nfe); Associated with methylmalonic acidemia with homocystinuria, type cblJ.

What condition is associated with ABCD4 p.Arg579Gln (c.1736G>A)?

ABCD4 p.Arg579Gln (c.1736G>A) is associated with methylmalonic acidemia with homocystinuria, type cblJ (ClinVar).

How common is ABCD4 p.Arg579Gln (c.1736G>A) in the general population?

ABCD4 p.Arg579Gln (c.1736G>A) is rare (popmax 0.575%, nfe) (gnomAD).

How is Methylmalonic acidemia with homocystinuria inherited?

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

What do computational predictors say about ABCD4 p.Arg579Gln (c.1736G>A)?

AlphaMissense predicts ambiguous (score 0.5386) — an in-silico prediction, not a clinical call.

ABCD4 p.Arg579Gln

c.1736G>A · rs143288344 · VCV376915

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

AlphaMissense

ambiguous

0.5386 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.575%, nfe)

Missense predictors

2/2 damaging

REVEL, SaProt · AlphaMissense no call

Conditions

methylmalonic acidemia with homocystinuria, type cblJ

Computational evidence

Protein change
AlphaMissense	0.5386	ambiguous
REVEL	0.927	moderately pathogenic-leaning
SaProt	LLR -11.17	damaging
⇒ REVEL and SaProt both call this damaging; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 2.3, phastCons 1
Regional constraint	o/e 0.99	unconstrained · MANE · 16 kb · p 0.79 · regional, not allelic
Overall
CADD	32.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.575% European (non-Finnish) · 6,789/1,180,030 alleles

Filtering AF 0.564% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.559%

Overall 0.514% 8,298/1,614,076 alleles · rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	1.72%	58
European (non-Finnish)grpmax	0.575%	174
Remaining individualsnot grpmax-eligible	0.362%	277
Admixed American	0.152%	660
African / African-American	0.0933%	1,072
South Asian	0.0231%	4,337
Middle Eastern	0.0165%	6,062
Ashkenazi Jewishnot grpmax-eligible	0.00675%	14,804

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: ABCD4
Protein: p.Arg579Gln
Coding: c.1736G>A
MANE Select: NM_005050
dbSNP: rs143288344
Type: single nucleotide variant
Location: chr14:74286717 (GRCh38)
Gene constraint: LOEUF 0.772 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.18 · 4 PDB
Residue 579: the abc transporter domain

Full ABCD4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

methylmalonic acidemia with homocystinuria, type cblJ — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Methylmalonic acidemia with homocystinuria (Orphanet):

Inheritance: Autosomal recessive, X-linked recessive
Onset: All ages

Similar variants

ABCD4 p.Arg579= Likely benign ★★ same residue
ABCD4 c.542+1G>T Pathogenic ★★ same condition
ABCD4 p.Arg432Gln Likely pathogenic ★★ same condition
ABCD4 p.Asn141Lys Pathogenic/Likely pathogenic ★★ same condition
ABCD4 p.Gln530Ter Pathogenic/Likely pathogenic ★★ same condition
ABCD4 p.Tyr176Ter Pathogenic/Likely pathogenic ★★ same condition
ABCD4 c.1028+5G>A Uncertain significance ★★ same condition
ABCD4 c.425+6C>T 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/abcd4-p-arg579gln (accessed [today's date]).

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