Is LTBP3 p.Pro556= (c.1668G>A) pathogenic?

LTBP3 p.Pro556= (c.1668G>A) is classified Likely benign in LTBP3 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-08-11). Very rare (popmax 0.002%, nfe); Associated with Inborn genetic diseases.

What condition is associated with LTBP3 p.Pro556= (c.1668G>A)?

LTBP3 p.Pro556= (c.1668G>A) is associated with Inborn genetic diseases, brachyolmia-amelogenesis imperfecta syndrome (ClinVar).

How common is LTBP3 p.Pro556= (c.1668G>A) in the general population?

LTBP3 p.Pro556= (c.1668G>A) is very rare (popmax 0.002%, nfe) (gnomAD).

LTBP3 p.Pro556=

c.1668G>A · rs1029967686 · VCV1777612

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.002%, nfe)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.052	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -4	GERP -3.5
Overall
CADD	1.698	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.002% European (non-Finnish) · 23/1,148,572 alleles

Filtering AF 0.00133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00111%

Overall 0.00155% 24/1,552,680 alleles · very rare exomes 24/1,400,402 · genomes 0/152,278 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.002%	49,938
South Asian	0.00119%	84,210

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: LTBP3
Protein: p.Pro556=
Coding: c.1668G>A
MANE Select: NM_001130144
dbSNP: rs1029967686
Type: single nucleotide variant
Location: chr11:65551178 (GRCh38)
Gene constraint: LOEUF 0.824 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 64.21

Full LTBP3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: brachyolmia-amelogenesis imperfecta syndrome

Similar variants

LTBP3 p.Pro556Arg Uncertain significance ★★ ⚠ same residue
LTBP3 p.Pro556Ser Uncertain significance ★ ⚠ same residue
LTBP3 c.1063+1G>T Likely pathogenic ★★ same condition
LTBP3 c.3629-3C>T Uncertain significance ★★ same condition
LTBP3 c.3761-2A>G Uncertain significance ★★ same condition
LTBP3 p.Ala1149Thr Uncertain significance ★★ ⚠ same condition
LTBP3 p.Ala1153Val Uncertain significance ★★ ⚠ same condition
LTBP3 p.Ala1182Val 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/ltbp3-p-pro556 (accessed [today's date]).

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