CSF2RB p.Pro830=
c.2490C>T · rs143285765 · VCV1582803
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.045%, sas)
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 -0.24 | GERP -3.3, phastCons 0.011 |
| Overall | ||
| CADD | 0.116 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.045%
South Asian · 41/91,080 alleles
Filtering AF
0.034%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0319%
Overall
0.0303%
489/1,614,206 alleles · ultra-rare
exomes 457/1,461,874 · genomes 32/152,332 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.045% | 2,221 |
| European (non-Finnish) | 0.0358% | 2,790 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,209 |
| African / African-American | 0.00799% | 12,510 |
| Admixed American | 0.00666% | 15,008 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,604 |
| East Asian | 0.00223% | 44,880 |
| Finnishnot grpmax-eligible | 0.00156% | 64,032 |
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
- CSF2RB
- Protein
- p.Pro830=
- Coding
- c.2490C>T
- MANE Select
- NM_000395
- dbSNP
- rs143285765
- Type
- single nucleotide variant
- Location
- chr22:36938298 (GRCh38)
- Gene constraint
- LOEUF 0.511 · pLI 0.93 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 65.50 · 10 PDB
- Residue 830
- the 'disordered' region
Similar variants
- CSF2RB p.Pro830Ser Uncertain significance ★ ⚠ same residue
- CSF2RB p.Ala185Thr Uncertain significance ★★ ⚠ same type
- CSF2RB p.Ala255Thr Uncertain significance ★★ ⚠ same type
- CSF2RB p.Ala314Thr Uncertain significance ★★ ⚠ same type
- CSF2RB p.Ala314Val Uncertain significance ★★ ⚠ same type
- CSF2RB p.Ala394Thr Uncertain significance ★★ ⚠ same type
- CSF2RB p.Ala455Thr Uncertain significance ★★ ⚠ same type
- CSF2RB p.Ala576Thr 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/csf2rb-p-pro830 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown