Is LTBP2 p.Phe1729= (c.5187C>T) pathogenic?

LTBP2 p.Phe1729= (c.5187C>T) is classified Conflicting classifications of pathogenicity in LTBP2 (ClinVar, Conflicting submitters, 4 submitters; last evaluated 2026-01-26). Low-frequency (popmax 1.62%, afr); Associated with Weill-Marchesani syndrome.

What condition is associated with LTBP2 p.Phe1729= (c.5187C>T)?

LTBP2 p.Phe1729= (c.5187C>T) is associated with Weill-Marchesani syndrome, glaucoma 3, primary congenital, D (ClinVar).

How common is LTBP2 p.Phe1729= (c.5187C>T) in the general population?

LTBP2 p.Phe1729= (c.5187C>T) is low-frequency (popmax 1.62%, afr) (gnomAD).

LTBP2 p.Phe1729=

c.5187C>T · rs149587738 · VCV731624

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.62%, afr)

Conditions

Weill-Marchesani syndrome

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 -3.8	GERP -3.5
Overall
CADD	3.766	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.62% African / African-American · 1,217/75,034 alleles

Filtering AF 1.55% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.52%

Overall 0.0852% 1,375/1,614,082 alleles · low-frequency exomes 676/1,461,802 · genomes 699/152,280 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.62%	62
Remaining individualsnot grpmax-eligible	0.112%	893
Middle Eastern	0.099%	1,010
Admixed American	0.095%	1,053
South Asian	0.0143%	7,007
East Asian	0.00669%	14,955
European (non-Finnish)	0.000763%	131,115

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: LTBP2
Protein: p.Phe1729=
Coding: c.5187C>T
MANE Select: NM_000428
dbSNP: rs149587738
Type: single nucleotide variant
Location: chr14:74501574 (GRCh38)
Gene constraint: LOEUF 0.595 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 58.33
Residue 1729: the 'c-terminal domain' region

Full LTBP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Weill-Marchesani syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: glaucoma 3, primary congenital, D

Similar variants

LTBP2 c.2389-2A>G Likely pathogenic ★★ same condition
LTBP2 p.Arg299Ter Pathogenic ★★ same condition
LTBP2 p.Cys1438Tyr Likely pathogenic ★★ same condition
LTBP2 c.-55G>A Uncertain significance ★★ same condition
LTBP2 c.-93C>T Uncertain significance ★★ same condition
LTBP2 c.*229C>T Uncertain significance ★★ same condition
LTBP2 p.Ala1359Thr Uncertain significance ★★ same condition
LTBP2 p.Ala733Thr 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/ltbp2-p-phe1729 (accessed [today's date]).

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