CSMD3 p.Ile1850Phe
c.5548A>T · VCV4657184
Computational evidence
| Protein change | ||
| AlphaMissense | 0.4686 | ambiguous |
|---|---|---|
| REVEL | 0.299 | indeterminate |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.9 | GERP 1.5, phastCons 1 |
| Regional constraint | o/e 0.96 | unconstrained · MANE · 442 kb · p 0.031 · regional, not allelic |
| Overall | ||
| CADD | 22.5 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
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
- CSMD3
- Protein
- p.Ile1850Phe
- Coding
- c.5548A>T
- MANE Select
- NM_198123
- Type
- single nucleotide variant
- Location
- chr8:112408375 (GRCh38)
- Gene constraint
- LOEUF 0.464 · pLI 0.97 (gnomAD)
- Residue 1850
- the cub 10 domain
Similar variants
- CSMD3 p.Glu2761Val Uncertain significance ★★ same type
- CSMD3 p.Leu3027Phe Uncertain significance ★★ same type
- CSMD3 c.4896-3C>T Benign ★★ same type
- CSMD3 p.Arg1020His Benign ★★ same type
- CSMD3 p.Arg1228Gln Likely benign ★★ same type
- CSMD3 p.Arg687= Benign/Likely benign ★★ same type
- CSMD3 p.Asp1025= Benign ★★ same type
- CSMD3 p.Asp1473= Benign ★★ 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/csmd3-p-ile1850phe (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown