FLRT1 p.Tyr576=
c.1728C>T · rs35851449 · VCV461795
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.05%, afr)
Conditions
1
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 |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -14 | GERP -4 |
| Overall | ||
| CADD | 0.904 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.05%
African / African-American · 3,036/75,052 alleles
Filtering AF
3.93%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.88%
Overall
0.252%
4,074/1,613,774 alleles · low-frequency
exomes 2,183/1,461,458 · genomes 1,891/152,316 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.05% | 25 |
| Admixed American | 0.528% | 189 |
| Remaining individualsnot grpmax-eligible | 0.4% | 250 |
| Middle Eastern | 0.363% | 276 |
| Ashkenazi Jewishnot grpmax-eligible | 0.321% | 312 |
| European (non-Finnish) | 0.0291% | 3,440 |
| South Asian | 0.0121% | 8,281 |
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.Tyr576=
- Coding
- c.1728C>T
- MANE Select
- NM_013280
- dbSNP
- rs35851449
- Type
- single nucleotide variant
- Location
- chr11:64117995 (GRCh38)
- Gene constraint
- LOEUF 0.682 · pLI 0.14 (gnomAD)
- Structure
- AlphaFold pLDDT 73.46
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-tyr576 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown