FLVCR2 c.1024del
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.53e-05%, nfe)
Conditions
1
Fowler syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 9.2 | GERP 2.3, phastCons 1 |
| Non-coding constraint | Z 1.48 | 1 kb window · o/e 0.89 · regional · uncalibrated |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.53e-05%
European (non-Finnish) · 1/1,171,836 alleles
Overall
6.23e-05%
1/1,604,924 alleles · very rare
exomes 1/1,452,644 · genomes 0/152,280 · joint denominator
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
- FLVCR2
- Coding
- c.1024del
- MANE Select
- NM_017791
- Type
- Deletion
- Location
- chr14:75634909 (GRCh38)
- Gene constraint
- LOEUF 0.9 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 81.31 · 5 PDB
Similar variants
- FLVCR2 p.Leu64fs Likely pathogenic ★ same condition
- FLVCR2 p.Glu18fs Pathogenic/Likely pathogenic ★★ same condition
- FLVCR2 p.Thr430Arg Pathogenic/Likely pathogenic ★★ same condition
- FLVCR2 p.Arg84His Uncertain significance ★★ ⚠ same condition
- FLVCR2 p.Gly440Ser Uncertain significance ★★ ⚠ same condition
- FLVCR2 p.Ser216= Benign ★★ same condition
- FLVCR2 p.Gly469fs Likely pathogenic ★ same condition
- FLVCR2 p.Trp367Ter Pathogenic ★ 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/flvcr2-c-1024del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown