Is FLRT1 p.Tyr114= (c.342C>T) pathogenic?

FLRT1 p.Tyr114= (c.342C>T) is classified Likely benign in FLRT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-17). Ultra-rare (popmax 0.0535%, eas); Associated with peripheral neuropathy.

What condition is associated with FLRT1 p.Tyr114= (c.342C>T)?

FLRT1 p.Tyr114= (c.342C>T) is associated with peripheral neuropathy (ClinVar).

How common is FLRT1 p.Tyr114= (c.342C>T) in the general population?

FLRT1 p.Tyr114= (c.342C>T) is ultra-rare (popmax 0.0535%, eas) (gnomAD).

FLRT1 p.Tyr114=

c.342C>T · rs772794847 · VCV1127499

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0535%, 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 -9.8	GERP -4
Overall
CADD	0.936	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0535% East Asian · 24/44,896 alleles

Filtering AF 0.0368% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0313%

Overall 0.00279% 45/1,614,086 alleles · ultra-rare exomes 37/1,461,862 · genomes 8/152,224 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0535%	1,871
Finnishnot grpmax-eligible	0.00312%	32,009
African / African-American	0.00267%	37,467
Remaining individualsnot grpmax-eligible	0.0016%	62,484
European (non-Finnish)	0.00127%	78,670
South Asian	0.0011%	91,088

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.Tyr114=
Coding: c.342C>T
MANE Select: NM_013280
dbSNP: rs772794847
Type: single nucleotide variant
Location: chr11:64116609 (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-tyr114 (accessed [today's date]).

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