BICRA p.Pro983=
c.2949G>A · VCV3257636
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0173%, mid)
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 -3.3 | GERP -1.4 |
| Overall | ||
| CADD | 0.178 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0173%
Middle Eastern · 1/5,796 alleles
Filtering AF
0.00111%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000507%
Overall
0.0011%
17/1,545,240 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0173% | 5,796 |
| African / African-American | 0.00417% | 23,984 |
| South Asian | 0.00238% | 41,974 |
| European (non-Finnish) | 0.000954% | 104,819 |
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
- BICRA
- Protein
- p.Pro983=
- Coding
- c.2949G>A
- MANE Select
- NM_001394372
- Type
- single nucleotide variant
- Location
- chr19:47694953 (GRCh38)
- Gene constraint
- LOEUF 0.659 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 42.79
- Residue 983
- a UniProt-annotated variant site (in css12); the 'disordered' region
Similar variants
- BICRA p.Pro983Leu Uncertain significance ★★ ⚠ same residue
- BICRA p.Gln290Ter Pathogenic/Likely pathogenic ★★ same type
- BICRA p.Ala1110Thr Uncertain significance ★★ ⚠ same type
- BICRA p.Ala313Pro Uncertain significance ★★ ⚠ same type
- BICRA p.Ala579Thr Uncertain significance ★★ ⚠ same type
- BICRA p.Arg1384Cys Uncertain significance ★★ ⚠ same type
- BICRA p.Arg802Cys Uncertain significance ★★ ⚠ same type
- BICRA p.Asn408Lys 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/bicra-p-pro983 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown