Is ABCD1 p.Ser656Pro (c.1966T>C) pathogenic?

ABCD1 p.Ser656Pro (c.1966T>C) is classified Conflicting classifications of pathogenicity in ABCD1 (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2022-10-07). AlphaMissense: likely pathogenic (0.9972); Absent from gnomAD v4.1; Associated with ABCD1-related disorder.

What condition is associated with ABCD1 p.Ser656Pro (c.1966T>C)?

ABCD1 p.Ser656Pro (c.1966T>C) is associated with ABCD1-related disorder, adrenoleukodystrophy (ClinVar).

How common is ABCD1 p.Ser656Pro (c.1966T>C) in the general population?

ABCD1 p.Ser656Pro (c.1966T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ABCD1 p.Ser656Pro (c.1966T>C)?

AlphaMissense predicts likely pathogenic (score 0.9972) — an in-silico prediction, not a clinical call.

ABCD1 p.Ser656Pro

c.1966T>C · rs2148399307 · VCV1358174

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

AlphaMissense

likely pathogenic

0.9972 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,191,968)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

ABCD1-related disorder

Computational evidence

Protein change
AlphaMissense	0.9972	likely pathogenic · top 1% in ABCD1
REVEL	0.946	strongly pathogenic-leaning
SaProt	LLR -11.52	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 1.6, phastCons 1
Regional constraint	o/e 0.38	unconstrained · MANE · 3,261 bp · p 4e-11 · regional, not allelic
Overall
CADD	27.4	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

No allele count reported in gnomAD v4.1 (AN 1,191,968). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ABCD1
Protein: p.Ser656Pro
Coding: c.1966T>C
MANE Select: NM_000033
dbSNP: rs2148399307
Type: single nucleotide variant
Location: chrX:153743321 (GRCh38)
Structure: AlphaFold pLDDT 81.58 · 14 PDB
Residue 656: a β-strand; the abc transporter domain

Full ABCD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ABCD1-related disorder

Also linked: adrenoleukodystrophy

Similar variants

ABCD1 p.Ser656Phe Likely pathogenic ★★ same residue
ABCD1 p.Ser656= Likely benign ★ same residue
ABCD1 c.1635-2A>G Pathogenic ★★ same condition
ABCD1 c.1781-1G>C Pathogenic ★★ same condition
ABCD1 c.1781-1G>T Pathogenic/Likely pathogenic ★★ same condition
ABCD1 c.1866-10G>A Pathogenic/Likely pathogenic ★★ same condition
ABCD1 c.1866-1G>C Likely pathogenic ★★ same condition
ABCD1 c.1866-2A>T Likely pathogenic ★★ 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/abcd1-p-ser656pro (accessed [today's date]).

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