Is LTBP3 p.Pro13= (c.39T>C) pathogenic?

LTBP3 p.Pro13= (c.39T>C) is classified Likely benign in LTBP3 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-06-09). Very rare (popmax 0.00468%, sas); Associated with Inborn genetic diseases.

What condition is associated with LTBP3 p.Pro13= (c.39T>C)?

LTBP3 p.Pro13= (c.39T>C) is associated with Inborn genetic diseases (ClinVar).

How common is LTBP3 p.Pro13= (c.39T>C) in the general population?

LTBP3 p.Pro13= (c.39T>C) is very rare (popmax 0.00468%, sas) (gnomAD).

LTBP3 p.Pro13=

c.39T>C · VCV4859323

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00468%, sas)

Conditions

Inborn genetic diseases

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 2.4	GERP 0.071, phastCons 1
Overall
CADD	13.5	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00468% South Asian · 2/42,690 alleles

Filtering AF 0.000776% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000291%

Overall 0.000183% 2/1,092,208 alleles · very rare

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.Pro13=
Coding: c.39T>C
MANE Select: NM_001130144
Type: single nucleotide variant
Location: chr11:65557921 (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

Similar variants

LTBP3 p.Ala1149Thr Uncertain significance ★★ ⚠ same condition
LTBP3 p.Ala1153Val Uncertain significance ★★ ⚠ same condition
LTBP3 p.Ala1182Val Uncertain significance ★★ ⚠ same condition
LTBP3 p.Ala1250Pro Uncertain significance ★★ ⚠ same condition
LTBP3 p.Ala1289Val Uncertain significance ★★ ⚠ same condition
LTBP3 p.Ala144Ser Uncertain significance ★★ ⚠ same condition
LTBP3 p.Ala144Thr Uncertain significance ★★ ⚠ same condition
LTBP3 p.Ala147Val 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-pro13 (accessed [today's date]).

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