Is FLRT1 p.Arg586Gln (c.1757G>A) pathogenic?

FLRT1 p.Arg586Gln (c.1757G>A) is classified Uncertain significance in FLRT1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-05-28). Ultra-rare (popmax 0.07%, amr); Associated with peripheral neuropathy.

What condition is associated with FLRT1 p.Arg586Gln (c.1757G>A)?

FLRT1 p.Arg586Gln (c.1757G>A) is associated with peripheral neuropathy (ClinVar).

How common is FLRT1 p.Arg586Gln (c.1757G>A) in the general population?

FLRT1 p.Arg586Gln (c.1757G>A) is ultra-rare (popmax 0.07%, amr) (gnomAD).

FLRT1 p.Arg586Gln

c.1757G>A · rs762387650 · VCV941259

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.07%, amr)

Conditions

peripheral neuropathy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.013	strongly benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.14	GERP -1.7
Regional constraint	o/e 0.78	unconstrained · MANE · 2,021 bp · p 5.7e-12 · regional, not allelic
Overall
CADD	14.11	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.07% Admixed American · 42/60,008 alleles

Filtering AF 0.0532% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0473%

Overall 0.00545% 88/1,613,506 alleles · ultra-rare exomes 79/1,461,302 · genomes 9/152,204 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.07%	1,429
Ashkenazi Jewishnot grpmax-eligible	0.0304%	3,289
African / African-American	0.02%	4,996
Middle Eastern	0.0164%	6,084
Remaining individualsnot grpmax-eligible	0.0032%	31,230
South Asian	0.0022%	45,542
Finnishnot grpmax-eligible	0.00157%	63,596
European (non-Finnish)	0.00136%	73,746

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.Arg586Gln
Coding: c.1757G>A
MANE Select: NM_013280
dbSNP: rs762387650
Type: single nucleotide variant
Location: chr11:64118024 (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.Arg586Trp 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.Arg592Gln Uncertain significance ★★ same condition
FLRT1 p.Arg592Trp 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-arg586gln (accessed [today's date]).

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