Is LDB3 p.Pro164= (c.492G>A) pathogenic?

LDB3 p.Pro164= (c.492G>A) is classified Likely benign in LDB3 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-06-02). Very rare (popmax 0.00446%, eas); Associated with Cardiovascular phenotype.

What condition is associated with LDB3 p.Pro164= (c.492G>A)?

LDB3 p.Pro164= (c.492G>A) is associated with Cardiovascular phenotype, myofibrillar myopathy 4 (ClinVar).

How common is LDB3 p.Pro164= (c.492G>A) in the general population?

LDB3 p.Pro164= (c.492G>A) is very rare (popmax 0.00446%, eas) (gnomAD).

LDB3 p.Pro164=

c.492G>A · rs368407147 · VCV414133

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00446%, eas)

Conditions

Cardiovascular phenotype

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 -0.4	GERP -4.1
Overall
CADD	1.651	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00446% East Asian · 2/44,862 alleles

Filtering AF 0.00111% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0009%

Overall 0.00167% 27/1,613,006 alleles · very rare exomes 27/1,460,674 · genomes 0/152,332 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00446%	22,431
Admixed American	0.00333%	29,999
European (non-Finnish)	0.0017%	58,987
Remaining individualsnot grpmax-eligible	0.0016%	62,468
African / African-American	0.00133%	75,056
South Asian	0.0011%	91,074

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: LDB3
Protein: p.Pro164=
Coding: c.492G>A
MANE Select: NM_007078
dbSNP: rs368407147
Type: single nucleotide variant
Location: chr10:86681606 (GRCh38)
Gene constraint: LOEUF 0.864 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.98 · 2 PDB
Residue 164: the 'disordered' region

Full LDB3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: myofibrillar myopathy 4

Similar variants

LDB3 p.Asp164His Uncertain significance ★★ same residue
LDB3 p.Pro164Leu Uncertain significance ★★ ⚠ same residue
LDB3 p.Ala147Thr Pathogenic/Likely pathogenic ★★ same condition
LDB3 p.Ala165Val Pathogenic/Likely pathogenic ★★ same condition
LDB3 c.1231+4A>C Uncertain significance ★★ same condition
LDB3 c.1858-11C>A Uncertain significance ★★ same condition
LDB3 c.246-3C>T Uncertain significance ★★ same condition
LDB3 c.322-1G>A 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/ldb3-p-pro164 (accessed [today's date]).

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