Is FLRT1 p.Phe36= (c.108C>T) pathogenic?

FLRT1 p.Phe36= (c.108C>T) is classified Benign in FLRT1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2022-09-19). Rare (popmax 0.825%, mid); Associated with peripheral neuropathy.

What condition is associated with FLRT1 p.Phe36= (c.108C>T)?

FLRT1 p.Phe36= (c.108C>T) is associated with peripheral neuropathy (ClinVar).

How common is FLRT1 p.Phe36= (c.108C>T) in the general population?

FLRT1 p.Phe36= (c.108C>T) is rare (popmax 0.825%, mid) (gnomAD).

FLRT1 p.Phe36=

c.108C>T · rs200588570 · VCV461792

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.825%, mid)

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 0.21	GERP -0.67, phastCons 0.81
Overall
CADD	7.879	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.825% Middle Eastern · 50/6,062 alleles

Filtering AF 0.643% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.578%

Overall 0.166% 2,683/1,613,646 alleles · rare exomes 2,429/1,461,282 · genomes 254/152,364 · joint denominator

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	3.33%	30
Middle Easterngrpmax	0.825%	121
Remaining individualsnot grpmax-eligible	0.379%	264
Admixed American	0.192%	522
South Asian	0.114%	875
Amishnot grpmax-eligible	0.11%	912
European (non-Finnish)	0.0978%	1,022
African / African-American	0.032%	3,127
Finnishnot grpmax-eligible	0.0204%	4,895

Ashkenazi Jewish 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.Phe36=
Coding: c.108C>T
MANE Select: NM_013280
dbSNP: rs200588570
Type: single nucleotide variant
Location: chr11:64116375 (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-phe36 (accessed [today's date]).

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