Is ABCD4 p.Gln541Glu (c.1621C>G) pathogenic?

ABCD4 p.Gln541Glu (c.1621C>G) is classified Uncertain significance in ABCD4 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-08-01). AlphaMissense: likely benign (0.2019); Absent from gnomAD v4.1.

How common is ABCD4 p.Gln541Glu (c.1621C>G) in the general population?

ABCD4 p.Gln541Glu (c.1621C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ABCD4 p.Gln541Glu (c.1621C>G)?

AlphaMissense predicts likely benign (score 0.2019) — an in-silico prediction, not a clinical call.

ABCD4 p.Gln541Glu

c.1621C>G · rs2080235685 · VCV872053

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2019 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.2019	likely benign
REVEL	0.535	indeterminate
SaProt	LLR -8.47	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 12	GERP 2.6, phastCons 1
Regional constraint	o/e 0.99	unconstrained · MANE · 16 kb · p 0.79 · regional, not allelic
Overall
CADD	24.7	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: ABCD4
Protein: p.Gln541Glu
Coding: c.1621C>G
MANE Select: NM_005050
dbSNP: rs2080235685
Type: single nucleotide variant
Location: chr14:74287825 (GRCh38)
Gene constraint: LOEUF 0.772 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.18 · 4 PDB
Residue 541: the abc transporter domain

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

Similar variants

ABCD4 c.542+1G>T Pathogenic ★★ same type
ABCD4 p.Arg432Gln Likely pathogenic ★★ same type
ABCD4 p.Asn141Lys Pathogenic/Likely pathogenic ★★ same type
ABCD4 p.Gln530Ter Pathogenic/Likely pathogenic ★★ same type
ABCD4 p.Tyr176Ter Pathogenic/Likely pathogenic ★★ same type
ABCD4 c.1028+5G>A Uncertain significance ★★ same type
ABCD4 c.425+6C>T Uncertain significance ★★ same type
ABCD4 c.719+6T>C 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/abcd4-p-gln541glu (accessed [today's date]).

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