DAAM2 p.Arg445Ter
c.1333C>T · rs1764951663 · VCV1054670
Pathogenic
No assertion criteria
Classification
Pathogenic
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
nephrotic syndrome, type 24
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 12 of 25 |
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 1 | GERP -1.5, phastCons 1 |
| Overall | ||
| CADD | 37.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
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
- DAAM2
- Protein
- p.Arg445Ter
- Coding
- c.1333C>T
- MANE Select
- NM_001201427
- dbSNP
- rs1764951663
- Type
- single nucleotide variant
- Location
- chr6:39878234 (GRCh38)
- Gene constraint
- LOEUF 0.488 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 80.02
- Residue 445
- a UniProt-annotated variant site (in nphs24; affects the regulation of filopodia formation)
Similar variants
- DAAM2 p.Arg445Gln Uncertain significance ★ ⚠ same residue
- DAAM2 p.Arg335Trp Uncertain significance ★★ ⚠ same condition
- DAAM2 p.Arg676Trp Uncertain significance ★★ ⚠ same condition
- DAAM2 p.Arg990Cys Uncertain significance ★★ ⚠ same condition
- DAAM2 p.Gln760Arg Uncertain significance ★★ ⚠ same condition
- DAAM2 p.Pro74Thr Uncertain significance ★★ ⚠ same condition
- DAAM2 p.Arg66Ter Likely pathogenic ★ same condition
- DAAM2 p.Gly1020Ter Likely pathogenic ★ 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/daam2-p-arg445ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown