Is ABLIM2 p.Arg428Trp (c.1282C>T) pathogenic?

ABLIM2 p.Arg428Trp (c.1282C>T) is classified Uncertain significance in ABLIM2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-12). AlphaMissense: ambiguous (0.4975); Ultra-rare (popmax 0.0532%, nfe).

How common is ABLIM2 p.Arg428Trp (c.1282C>T) in the general population?

ABLIM2 p.Arg428Trp (c.1282C>T) is ultra-rare (popmax 0.0532%, nfe) (gnomAD).

What do computational predictors say about ABLIM2 p.Arg428Trp (c.1282C>T)?

AlphaMissense predicts ambiguous (score 0.4975) — an in-silico prediction, not a clinical call.

ABLIM2 p.Arg428Trp

c.1282C>T · VCV3793654

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4975 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0532%, nfe)

Computational evidence

Protein change
AlphaMissense	0.4975	ambiguous
REVEL	0.464	indeterminate
SaProt	LLR -11.66	damaging
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>T here scores Δ0.29 · evaluated, not missing
Constraint at this position
Conservation	phyloP 11	GERP 1.7, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 192 kb · p 0.27 · regional, not allelic
Overall
CADD	34.0	PHRED · no single calibrated threshold — expert panels disagree

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM R395W vs ClinVar R428W) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0532% European (non-Finnish) · 628/1,179,742 alleles

Filtering AF 0.0498% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0484%

Overall 0.0421% 679/1,613,522 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0532%	1,879
Remaining individualsnot grpmax-eligible	0.0432%	2,312
Admixed American	0.0267%	3,749
African / African-American	0.008%	12,502
East Asian	0.00223%	44,880
South Asian	0.0011%	90,928

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: ABLIM2
Protein: p.Arg428Trp
Coding: c.1282C>T
MANE Select: NM_001130083
Type: single nucleotide variant
Location: chr4:8020289 (GRCh38)
Gene constraint: LOEUF 0.743 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 66.21 · 3 PDB
Residue 428: the 'disordered' region

Full ABLIM2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABLIM2 c.763+4C>T Benign ★★ same type
ABLIM2 c.763+5A>G Benign ★★ same type
ABLIM2 p.Ala144Thr Uncertain significance ★ ⚠ same type
ABLIM2 p.Ala21Val Uncertain significance ★ ⚠ same type
ABLIM2 p.Ala288Val Uncertain significance ★ ⚠ same type
ABLIM2 p.Ala476Ser Uncertain significance ★ ⚠ same type
ABLIM2 p.Ala565Asp Uncertain significance ★ ⚠ same type
ABLIM2 p.Ala97Val 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/ablim2-p-arg428trp (accessed [today's date]).

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