RPRD2 p.Ala982=
c.2946C>T · VCV3947611
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00703%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.103 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -6.5 | GERP -3.3 |
| Overall | ||
| CADD | 4.798 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00703%
European (non-Finnish) · 83/1,179,892 alleles
Filtering AF
0.00579%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00533%
Overall
0.00595%
96/1,613,830 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00703% | 14,216 |
| East Asian | 0.00668% | 14,963 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,617 |
| South Asian | 0.00439% | 22,771 |
| African / African-American | 0.00267% | 37,442 |
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
- RPRD2
- Protein
- p.Ala982=
- Coding
- c.2946C>T
- MANE Select
- NM_015203
- Type
- single nucleotide variant
- Location
- chr1:150471894 (GRCh38)
- Gene constraint
- LOEUF 0.145 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 48.32 · 3 PDB
- Residue 982
- the 'disordered' region
Similar variants
- RPRD2 p.Glu195= Benign ★★ same type
- RPRD2 p.Ala1083Ser Uncertain significance ★ ⚠ same type
- RPRD2 p.Ala1145Pro Uncertain significance ★ ⚠ same type
- RPRD2 p.Ala1149Val Uncertain significance ★ ⚠ same type
- RPRD2 p.Ala1165Val Uncertain significance ★ ⚠ same type
- RPRD2 p.Ala1251Thr Uncertain significance ★ ⚠ same type
- RPRD2 p.Ala140Val Uncertain significance ★ ⚠ same type
- RPRD2 p.Ala442Pro 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/rprd2-p-ala982 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown