CPSF1 p.Gly306Val
c.917G>T · VCV3269268
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
ambiguous
0.4526 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
0/2 damaging
REVEL, SaProt · AlphaMissense no call
Computational evidence
| Protein change | ||
| AlphaMissense | 0.4526 | ambiguous |
|---|---|---|
| REVEL | 0.184 | benign-leaning |
| SaProt | LLR -3.04 | tolerated |
| ⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call. | ||
| Splicing | ||
| SpliceAI | Δ0.43 | donor gain · deltas |
| Constraint at this position | ||
| Conservation | phyloP 7.5 | GERP 1.9, phastCons 1 |
| Regional constraint | o/e 0.59 | unconstrained · MANE · 395 bp · p 2.5e-05 · regional, not allelic |
| Overall | ||
| CADD | 32.0 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CPSF1
- Protein
- p.Gly306Val
- Coding
- c.917G>T
- MANE Select
- NM_013291
- Type
- single nucleotide variant
- Location
- chr8:144400186 (GRCh38)
- Gene constraint
- LOEUF 0.74 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.97 · 13 PDB
- Residue 306
- a UniProt-annotated variant site (in myp27); a turn
Similar variants
- CPSF1 p.Ala1319Thr Uncertain significance ★★ ⚠ same type
- CPSF1 p.Thr561Ile Uncertain significance ★★ ⚠ same type
- CPSF1 p.Gly722= Likely benign ★★ same type
- CPSF1 p.Leu1360= Likely benign ★★ same type
- CPSF1 p.Pro438= Likely benign ★★ same type
- CPSF1 p.Pro654= Likely benign ★★ same type
- CPSF1 c.539+1G>A Likely pathogenic ★ same type
- CPSF1 c.1119+2T>G 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/cpsf1-p-gly306val (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown