Is FLRT1 p.Leu551= (c.1653G>A) pathogenic?

FLRT1 p.Leu551= (c.1653G>A) is classified Likely benign in FLRT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-12-19). Ultra-rare (popmax 0.033%, mid); Associated with peripheral neuropathy.

What condition is associated with FLRT1 p.Leu551= (c.1653G>A)?

FLRT1 p.Leu551= (c.1653G>A) is associated with peripheral neuropathy (ClinVar).

How common is FLRT1 p.Leu551= (c.1653G>A) in the general population?

FLRT1 p.Leu551= (c.1653G>A) is ultra-rare (popmax 0.033%, mid) (gnomAD).

FLRT1 p.Leu551=

c.1653G>A · rs373807742 · VCV706652

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.033%, mid)

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
Pangolin	Δ0.58	gain · loss 0.00 · not in the SpliceAI release · independent
Constraint at this position
Conservation	phyloP 3.6	GERP 0.4, phastCons 1
Overall
CADD	6.034	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.033% Middle Eastern · 2/6,062 alleles

Filtering AF 0.0193% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0184%

Overall 0.0182% 294/1,613,896 alleles · ultra-rare exomes 276/1,461,532 · genomes 18/152,364 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.033%	3,031
Remaining individualsnot grpmax-eligible	0.0304%	3,290
European (non-Finnish)	0.0215%	4,646
Admixed American	0.0117%	8,576
South Asian	0.00988%	10,120
African / African-American	0.004%	25,024

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.Leu551=
Coding: c.1653G>A
MANE Select: NM_013280
dbSNP: rs373807742
Type: single nucleotide variant
Location: chr11:64117920 (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.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
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-leu551 (accessed [today's date]).

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