Is FLRT1 p.Ala96= (c.288C>T) pathogenic?

FLRT1 p.Ala96= (c.288C>T) is classified Benign in FLRT1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-01-19). Common (popmax 67.9%, nfe) — too common for a highly-penetrant pathogenic allele; Associated with peripheral neuropathy.

What condition is associated with FLRT1 p.Ala96= (c.288C>T)?

FLRT1 p.Ala96= (c.288C>T) is associated with peripheral neuropathy (ClinVar).

FLRT1 p.Ala96=

Q: How common is FLRT1 p.Ala96= (c.288C>T) in the general population?

FLRT1 p.Ala96= (c.288C>T) is common (popmax 67.9%, nfe) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.288C>T · rs614035 · VCV1167055

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 67.9%, nfe) — too common for a highly-penetrant pathogenic allele

Conditions

peripheral neuropathy

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 -10	GERP -4
Overall
CADD	0.044	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 67.9% European (non-Finnish) · 801,007/1,179,916 alleles

Filtering AF 67.8% ClinGen BA1/BS1 input FAF95, joint · FAF99 67.7%

Overall 63.2% 1,019,520/1,613,820 alleles · common

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	75.5%	1
Finnishnot grpmax-eligible	71.6%	1
Ashkenazi Jewishnot grpmax-eligible	70.9%	1
European (non-Finnish)grpmax	67.9%	1
Middle Eastern	64.8%	2
Remaining individualsnot grpmax-eligible	61.4%	2
Admixed American	52.7%	2
South Asian	51.1%	2
East Asian	30.9%	3
African / African-American	22.2%	4

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Ala96=
Coding: c.288C>T
MANE Select: NM_014067 · reported on NM_013280
dbSNP: rs614035
Type: single nucleotide variant
Location: chr11:64116555 (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-ala96 (accessed [today's date]).

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