Is ABLIM2 p.Ala226= (c.678C>T) pathogenic?

ABLIM2 p.Ala226= (c.678C>T) is classified Likely benign in ABLIM2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-01). Rare (popmax 0.24%, afr).

How common is ABLIM2 p.Ala226= (c.678C>T) in the general population?

ABLIM2 p.Ala226= (c.678C>T) is rare (popmax 0.24%, afr) (gnomAD).

ABLIM2 p.Ala226=

c.678C>T · VCV4681369

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.24%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -20	GERP -3.8
Overall
CADD	0.005	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.24% African / African-American · 179/74,498 alleles

Filtering AF 0.211% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.2%

Overall 0.0196% 311/1,585,402 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.24%	416
South Asian	0.0496%	2,015
Middle Eastern	0.0336%	2,976
Admixed American	0.0324%	3,083
Remaining individualsnot grpmax-eligible	0.0293%	3,418
European (non-Finnish)	0.00438%	22,853

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.Ala226=
Coding: c.678C>T
MANE Select: NM_001130083
Type: single nucleotide variant
Location: chr4:8061052 (GRCh38)
Gene constraint: LOEUF 0.743 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 66.21 · 3 PDB
Residue 226: the lim zinc-binding 4 domain

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-ala226 (accessed [today's date]).

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