Is ABCA10 p.Arg1466Ser (c.4398A>T) pathogenic?

ABCA10 p.Arg1466Ser (c.4398A>T) is classified Uncertain significance in ABCA10 (ClinVar, Single submitter, 2 submitters; last evaluated 2024-01-30). AlphaMissense: likely benign (0.2849); Ultra-rare (popmax 0.0424%, eas).

How common is ABCA10 p.Arg1466Ser (c.4398A>T) in the general population?

ABCA10 p.Arg1466Ser (c.4398A>T) is ultra-rare (popmax 0.0424%, eas) (gnomAD).

What do computational predictors say about ABCA10 p.Arg1466Ser (c.4398A>T)?

AlphaMissense predicts likely benign (score 0.2849) — an in-silico prediction, not a clinical call.

ABCA10 p.Arg1466Ser

c.4398A>T · rs137945891 · VCV3080748

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.2849 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0424%, eas)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.2849	likely benign
REVEL	0.315	indeterminate
SaProt	LLR -6.70	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 -10	GERP -3.2
Regional constraint	o/e 0.95	unconstrained · MANE · 77 kb · p 0.045 · regional, not allelic
Overall
CADD	15.99	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 0.0424% East Asian · 19/44,790 alleles

Filtering AF 0.0277% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.023%

Overall 0.00155% 25/1,607,864 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0424%	2,357
Remaining individualsnot grpmax-eligible	0.00482%	20,763
South Asian	0.00332%	30,128

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: ABCA10
Protein: p.Arg1466Ser
Coding: c.4398A>T
MANE Select: NM_001377321
dbSNP: rs137945891
Type: single nucleotide variant
Location: chr17:69150063 (GRCh38)
Gene constraint: LOEUF 1.044 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.70

Full ABCA10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

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ABCA10 p.Ala1335Pro Uncertain significance ★ ⚠ same type
ABCA10 p.Ala1461Thr Uncertain significance ★ ⚠ same type
ABCA10 p.Ala244Ser Uncertain significance ★ ⚠ same type
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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/abca10-p-arg1466ser (accessed [today's date]).

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