Is FLRT1 p.Thr404= (c.1212G>A) pathogenic?

FLRT1 p.Thr404= (c.1212G>A) is classified Likely benign in FLRT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-16). Ultra-rare (popmax 0.0424%, eas); Associated with peripheral neuropathy.

What condition is associated with FLRT1 p.Thr404= (c.1212G>A)?

FLRT1 p.Thr404= (c.1212G>A) is associated with peripheral neuropathy (ClinVar).

How common is FLRT1 p.Thr404= (c.1212G>A) in the general population?

FLRT1 p.Thr404= (c.1212G>A) is ultra-rare (popmax 0.0424%, eas) (gnomAD).

FLRT1 p.Thr404=

c.1212G>A · rs764179577 · VCV772484

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0424%, eas)

Conditions

peripheral neuropathy

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -9.5	GERP -3.3
Overall
CADD	0.092	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0424% East Asian · 19/44,836 alleles

Filtering AF 0.0277% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.023%

Overall 0.00298% 48/1,612,416 alleles · ultra-rare exomes 42/1,460,068 · genomes 6/152,348 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0424%	2,360
Middle Eastern	0.0165%	6,052
Remaining individualsnot grpmax-eligible	0.00481%	20,801
Admixed American	0.00334%	29,976
European (non-Finnish)	0.00178%	56,133
Finnishnot grpmax-eligible	0.00156%	63,942
South Asian	0.0011%	90,960

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.Thr404=
Coding: c.1212G>A
MANE Select: NM_013280
dbSNP: rs764179577
Type: single nucleotide variant
Location: chr11:64117479 (GRCh38)

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

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-thr404 (accessed [today's date]).

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