Is FLRT1 p.Pro429= (c.1287C>T) pathogenic?

FLRT1 p.Pro429= (c.1287C>T) is classified Likely benign in FLRT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-12-06). Ultra-rare (popmax 0.0201%, amr); Associated with peripheral neuropathy.

What condition is associated with FLRT1 p.Pro429= (c.1287C>T)?

FLRT1 p.Pro429= (c.1287C>T) is associated with peripheral neuropathy (ClinVar).

How common is FLRT1 p.Pro429= (c.1287C>T) in the general population?

FLRT1 p.Pro429= (c.1287C>T) is ultra-rare (popmax 0.0201%, amr) (gnomAD).

FLRT1 p.Pro429=

c.1287C>T · rs543037879 · VCV1147502

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0201%, amr)

Conditions

peripheral neuropathy

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 0.088	GERP -3.7, phastCons 0.019
Overall
CADD	2.67	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0201% Admixed American · 12/59,562 alleles

Filtering AF 0.0116% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00904%

Overall 0.000934% 15/1,605,886 alleles · ultra-rare exomes 10/1,453,510 · genomes 5/152,376 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0201%	4,963
Remaining individualsnot grpmax-eligible	0.00161%	62,018
African / African-American	0.00133%	74,916
European (non-Finnish)	8.51e-05%	1,174,657

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: FLRT1
Protein: p.Pro429=
Coding: c.1287C>T
MANE Select: NM_013280
dbSNP: rs543037879
Type: single nucleotide variant
Location: chr11:64117554 (GRCh38)
Gene constraint: LOEUF 0.682 · pLI 0.14 (gnomAD)
Structure: AlphaFold pLDDT 73.46

Full FLRT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

peripheral neuropathy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

FLRT1 p.Pro429Leu Uncertain significance ★ same residue
FLRT1 p.Ala148Gly Uncertain significance ★★ same condition
FLRT1 p.Ala461Thr Uncertain significance ★★ same condition
FLRT1 p.Arg149Cys Uncertain significance ★★ same condition
FLRT1 p.Arg326Lys Uncertain significance ★★ same condition
FLRT1 p.Arg452His Uncertain significance ★★ same condition
FLRT1 p.Arg586Gln Uncertain significance ★★ same condition
FLRT1 p.Arg592Gln 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/flrt1-p-pro429 (accessed [today's date]).

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