Is LIMS2 p.Ala25= (c.75C>T) pathogenic?

LIMS2 p.Ala25= (c.75C>T) is classified Likely benign in LIMS2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-04). Ultra-rare (popmax 0.0401%, eas); Associated with autosomal recessive limb-girdle muscular dystrophy type 2W.

What condition is associated with LIMS2 p.Ala25= (c.75C>T)?

LIMS2 p.Ala25= (c.75C>T) is associated with autosomal recessive limb-girdle muscular dystrophy type 2W (ClinVar).

How common is LIMS2 p.Ala25= (c.75C>T) in the general population?

LIMS2 p.Ala25= (c.75C>T) is ultra-rare (popmax 0.0401%, eas) (gnomAD).

LIMS2 p.Ala25=

c.75C>T · rs199821222 · VCV778634

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0401%, eas)

Conditions

autosomal recessive limb-girdle muscular dystrophy type 2W

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -20	GERP -3.8
Overall
CADD	0.006	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0401% East Asian · 18/44,880 alleles

Filtering AF 0.0259% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0214%

Overall 0.00434% 70/1,613,282 alleles · ultra-rare exomes 68/1,460,922 · genomes 2/152,360 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0401%	2,493
South Asian	0.00879%	11,382
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,574
European (non-Finnish)	0.00331%	30,252
Remaining individualsnot grpmax-eligible	0.0032%	31,242
African / African-American	0.00266%	37,531

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: LIMS2
Protein: p.Ala25=
Coding: c.75C>T
MANE Select: NM_001161403
dbSNP: rs199821222
Type: single nucleotide variant
Location: chr2:127657499 (GRCh38)
Gene constraint: LOEUF 0.985 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.16 · 1 PDB
Residue 25: the lim zinc-binding 1 domain

Full LIMS2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

autosomal recessive limb-girdle muscular dystrophy type 2W — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

LIMS2 p.Ala25Thr Uncertain significance ★★ ⚠ same residue
LIMS2 c.11+1287G>T Uncertain significance ★★ same condition
LIMS2 c.11+1305G>A Uncertain significance ★★ same condition
LIMS2 c.12-6769C>G Uncertain significance ★★ same condition
LIMS2 c.754-2A>G Uncertain significance ★★ same condition
LIMS2 p.Ala110Val Uncertain significance ★★ ⚠ same condition
LIMS2 p.Ala212Val Uncertain significance ★★ ⚠ same condition
LIMS2 p.Ala44Thr Uncertain significance ★★ ⚠ 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/lims2-p-ala25 (accessed [today's date]).

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