Is ABCD4 p.Gln59Arg (c.176A>G) pathogenic?

ABCD4 p.Gln59Arg (c.176A>G) is classified Benign/Likely benign in ABCD4 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-02-04). AlphaMissense: likely benign (0.0938); Common (popmax 23.2%, afr) — too common for a highly-penetrant pathogenic allele; Associated with methylmalonic acidemia with homocystinuria, type cblJ.

What condition is associated with ABCD4 p.Gln59Arg (c.176A>G)?

ABCD4 p.Gln59Arg (c.176A>G) is associated with methylmalonic acidemia with homocystinuria, type cblJ (ClinVar).

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.Gln59Arg (c.176A>G)?

AlphaMissense predicts likely benign (score 0.0938) — an in-silico prediction, not a clinical call.

ABCD4 p.Gln59Arg

Q: How common is ABCD4 p.Gln59Arg (c.176A>G) in the general population?

ABCD4 p.Gln59Arg (c.176A>G) is common (popmax 23.2%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.176A>G · rs58272575 · VCV380496

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

AlphaMissense

likely benign

0.0938 · ACMG-weighted

gnomAD v4.1

Common

common (popmax 23.2%, afr) — too common for a highly-penetrant pathogenic allele

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

methylmalonic acidemia with homocystinuria, type cblJ

Computational evidence

Protein change
AlphaMissense	0.0938	likely benign
REVEL	0.376	indeterminate
SaProt	LLR -6.72	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 0.13	GERP -3.4, phastCons 0.99
Regional constraint	o/e 0.99	unconstrained · MANE · 16 kb · p 0.79 · regional, not allelic
Overall
CADD	12.91	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 23.2% African / African-American · 17,403/74,922 alleles

Filtering AF 22.9% ClinGen BA1/BS1 input FAF95, joint · FAF99 22.8%

Overall 1.24% 19,944/1,612,992 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	23.2%	4
Remaining individualsnot grpmax-eligible	1.61%	62
Admixed American	1.51%	66
Middle Eastern	1.06%	95
South Asian	0.0462%	2,165
European (non-Finnish)	0.0445%	2,247
East Asian	0.00446%	22,434
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,568

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.Gln59Arg
Coding: c.176A>G
MANE Select: NM_005050
dbSNP: rs58272575
Type: single nucleotide variant
Location: chr14:74299657 (GRCh38)
Gene constraint: LOEUF 0.772 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.18 · 4 PDB
Residue 59: the abc transmembrane type-1 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 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
ABCD4 c.719+6T>C 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-gln59arg (accessed [today's date]).

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