CSF2RB p.Ser396=
c.1188C>T · rs753691107 · VCV1446112
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0822%, 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 0.77 | GERP 1.5, phastCons 0.29 |
| Overall | ||
| CADD | 9.357 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0822%
Middle Eastern · 5/6,082 alleles
Filtering AF
0.0323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.021%
Overall
0.00199%
32/1,610,446 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0822% | 1,216 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,607 |
| European (non-Finnish) | 0.00195% | 51,300 |
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.Ser396=
- Coding
- c.1188C>T
- MANE Select
- NM_000395
- dbSNP
- rs753691107
- Type
- single nucleotide variant
- Location
- chr22:36933867 (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 396
- the fibronectin type-iii 2 domain; a β-strand
Similar variants
- CSF2RB p.Ser396Thr 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-ser396 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown