Is LTBP3 p.Val591= (c.1773G>A) pathogenic?

LTBP3 p.Val591= (c.1773G>A) is classified Likely benign in LTBP3 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-11-24). Very rare (popmax 0.00134%, afr); Associated with Inborn genetic diseases.

What condition is associated with LTBP3 p.Val591= (c.1773G>A)?

LTBP3 p.Val591= (c.1773G>A) is associated with Inborn genetic diseases (ClinVar).

How common is LTBP3 p.Val591= (c.1773G>A) in the general population?

LTBP3 p.Val591= (c.1773G>A) is very rare (popmax 0.00134%, afr) (gnomAD).

LTBP3 p.Val591=

c.1773G>A · rs1856454660 · VCV1779837

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00134%, afr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.036	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.1	GERP -2, phastCons 1
Overall
CADD	3.735	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00134% African / African-American · 1/74,876 alleles

Overall 0.000124% 2/1,613,708 alleles · very rare exomes 1/1,461,610 · genomes 1/152,098 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00134%	74,876
European (non-Finnish)	8.47e-05%	1,179,997

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.Val591=
Coding: c.1773G>A
MANE Select: NM_001130144
dbSNP: rs1856454660
Type: single nucleotide variant
Location: chr11:65547993 (GRCh38)
Gene constraint: LOEUF 0.824 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 64.21
Residue 591: the egf-like 3 domain

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.Val591Met Uncertain significance ★ ⚠ same residue
LTBP3 p.Val591Ala Uncertain significance ★ ⚠ same residue
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

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-val591 (accessed [today's date]).

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