RANBP2 p.Asp1965=
c.5895C>T · VCV4956369
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000509%, nfe)
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 -0.92 | GERP -2.9, phastCons 0.003 |
| Overall | ||
| CADD | 4.499 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000509%
European (non-Finnish) · 6/1,179,842 alleles
Filtering AF
0.000183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00012%
Overall
0.000372%
6/1,611,890 alleles · very rare
exomes 6/1,459,686 · genomes 0/152,204 · 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
- RANBP2
- Protein
- p.Asp1965=
- Coding
- c.5895C>T
- MANE Select
- NM_006267
- Type
- single nucleotide variant
- Location
- chr2:108766434 (GRCh38)
- Gene constraint
- LOEUF 0.231 · pLI 1.00 (gnomAD)
- Residue 1965
- the '22 x 2 aa repeats of f-g' region
Similar variants
- RANBP2 p.Asp1965Asn Uncertain significance ★ same residue
- RANBP2 p.Asp1965fs Uncertain significance ★ same residue
- 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
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-asp1965 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown