RANBP2 p.Ser1707=
c.5121A>G · VCV4956359
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00412%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.051 | GERP -1.7 |
| Overall | ||
| CADD | 0.928 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00412%
African / African-American · 3/72,830 alleles
Filtering AF
0.00109%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000503%
Overall
0.000249%
4/1,604,848 alleles · very rare
exomes 1/1,458,500 · genomes 3/146,348 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00412% | 24,277 |
| South Asian | 0.0011% | 90,578 |
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
- RANBP2
- Protein
- p.Ser1707=
- Coding
- c.5121A>G
- MANE Select
- NM_006267
- Type
- single nucleotide variant
- Location
- chr2:108765660 (GRCh38)
- Gene constraint
- LOEUF 0.231 · pLI 1.00 (gnomAD)
- Residue 1707
- the '22 x 2 aa repeats of f-g' region; the 'disordered' region
Similar variants
- EDAR p.Arg358Gln Pathogenic/Likely pathogenic ★★ ⚠ same type
- RANBP2 p.Thr585Met Pathogenic/Likely pathogenic ★★ ⚠ same type
- EDAR p.Leu353Phe Uncertain significance ★★ ⚠ same type
- RANBP2 c.406-2A>G Uncertain significance ★★ same type
- RANBP2 p.Ala2337Val Uncertain significance ★★ same type
- RANBP2 p.Ala2564Ser Uncertain significance ★★ ⚠ same type
- RANBP2 p.Ala3072Val Uncertain significance ★★ ⚠ same type
- RANBP2 p.Ala534Val 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/ranbp2-p-ser1707 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown