FER p.Thr519=
c.1557T>C · rs34320303 · VCV792007
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.54%, afr)
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 1.2 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 8.656 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.54%
African / African-American · 2,653/74,922 alleles
Filtering AF
3.43%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.38%
Overall
0.181%
2,923/1,611,680 alleles · low-frequency
exomes 1,379/1,459,708 · genomes 1,544/151,972 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.54% | 28 |
| Remaining individualsnot grpmax-eligible | 0.189% | 529 |
| Admixed American | 0.174% | 575 |
| Middle Eastern | 0.132% | 756 |
| South Asian | 0.0044% | 22,726 |
| European (non-Finnish) | 0.00305% | 32,738 |
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
- FER
- Protein
- p.Thr519=
- Coding
- c.1557T>C
- MANE Select
- NM_005246
- dbSNP
- rs34320303
- Type
- single nucleotide variant
- Location
- chr5:108959248 (GRCh38)
- Gene constraint
- LOEUF 0.723 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.29 · 2 PDB
- Residue 519
- the sh2 domain
Similar variants
- FER p.Ala272Thr Uncertain significance ★ ⚠ same type
- FER p.Ala313Gly Uncertain significance ★ ⚠ same type
- FER p.Ala438Ser Uncertain significance ★ ⚠ same type
- FER p.Ala89Thr Uncertain significance ★ ⚠ same type
- FER p.Arg417Ser Uncertain significance ★ ⚠ same type
- FER p.Arg707His Uncertain significance ★ ⚠ same type
- FER p.Asn148Ile Uncertain significance ★ ⚠ same type
- FER p.Asn261Ser Uncertain significance ★ ⚠ same type
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/fer-p-thr519 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown