Is ABLIM1 p.Arg628Trp (c.1882C>T) pathogenic?

ABLIM1 p.Arg628Trp (c.1882C>T) is classified Uncertain significance in ABLIM1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-16). AlphaMissense: likely benign (0.2438); Very rare (popmax 0.00254%, nfe).

How common is ABLIM1 p.Arg628Trp (c.1882C>T) in the general population?

ABLIM1 p.Arg628Trp (c.1882C>T) is very rare (popmax 0.00254%, nfe) (gnomAD).

What do computational predictors say about ABLIM1 p.Arg628Trp (c.1882C>T)?

AlphaMissense predicts likely benign (score 0.2438) — an in-silico prediction, not a clinical call.

ABLIM1 p.Arg628Trp

c.1882C>T · rs1473633676 · VCV2387001

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2438 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00254%, nfe)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2438	likely benign
REVEL	0.172	moderately benign-leaning
SaProt	LLR -10.06	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.6	GERP -1.4, phastCons 1
Regional constraint	o/e 0.93	unconstrained · MANE · 7,842 bp · p 0.28 · regional, not allelic
Overall
CADD	26.6	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 0.00254% European (non-Finnish) · 30/1,179,658 alleles

Filtering AF 0.0018% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00157%

Overall 0.00198% 32/1,612,700 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00254%	39,322
Remaining individualsnot grpmax-eligible	0.0016%	62,432
South Asian	0.0011%	90,968

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: ABLIM1
Protein: p.Arg628Trp
Coding: c.1882C>T
MANE Select: NM_002313
dbSNP: rs1473633676
Type: single nucleotide variant
Location: chr10:114444080 (GRCh38)
Gene constraint: LOEUF 0.515 · pLI 0.70 (gnomAD)
Structure: AlphaFold pLDDT 59.86

Full ABLIM1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABLIM1 p.Arg628Gln Uncertain significance ★ ⚠ same residue
ABLIM1 p.Ala506Thr Uncertain significance ★★ ⚠ same type
ABLIM1 c.2060-2A>G Uncertain significance ★ same type
ABLIM1 c.379+1G>A Uncertain significance ★ same type
ABLIM1 p.Ala29Val Uncertain significance ★ ⚠ same type
ABLIM1 p.Ala51Thr Uncertain significance ★ ⚠ same type
ABLIM1 p.Ala55Gly Uncertain significance ★ ⚠ same type
ABLIM1 p.Ala83Val 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/ablim1-p-arg628trp (accessed [today's date]).

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