CSF2RA p.Asp64Gly
c.191A>G · rs150743648 · VCV573103
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.138 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.96 | GERP -0.41, phastCons 0.002 |
| Regional constraint | o/e 1.06 | unconstrained · MANE · 27 kb · p 0.2 · regional, not allelic |
| Overall | ||
| CADD | 4.619 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Amishnot grpmax-eligible | 0.548% | 182 |
| Admixed Americangrpmax | 0.162% | 618 |
| Middle Eastern | 0.0661% | 1,514 |
| European (non-Finnish) | 0.0564% | 1,774 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0439% | 2,277 |
| Remaining individualsnot grpmax-eligible | 0.0304% | 3,289 |
| African / African-American | 0.00533% | 18,751 |
| South Asian | 0.0011% | 91,078 |
Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
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
- CSF2RA
- Protein
- p.Asp64Gly
- Coding
- c.191A>G
- MANE Select
- NM_172245
- dbSNP
- rs150743648
- Type
- single nucleotide variant
- Location
- chrX:1285892 (GRCh38)
- Structure
- AlphaFold pLDDT 82.15 · 2 PDB
- Residue 64
- a β-strand
Disease context
surfactant metabolism dysfunction, pulmonary, 4 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Hereditary pulmonary alveolar proteinosis (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adolescent, Adult, Childhood, Elderly, Infancy
- Prevalence
- <1 / 1 000 000 (Worldwide)
Similar variants
- CSF2RA p.Arg199Ter Pathogenic ★★ same condition
- CSF2RA p.Arg217Ter Pathogenic/Likely pathogenic ★★ same condition
- CSF2RA p.Gln204Ter Pathogenic ★★ same condition
- CSF2RA p.Gln263Ter Pathogenic/Likely pathogenic ★★ same condition
- CSF2RA p.Arg354Gln Uncertain significance ★★ same condition
- CSF2RA p.Gly339Val Uncertain significance ★★ same condition
- CSF2RA p.Gly386Arg Uncertain significance ★★ same condition
- CSF2RA p.Leu336Val Uncertain significance ★★ same condition
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/csf2ra-p-asp64gly (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown