AGPS p.Asn272fs
c.815del · VCV4815256
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
rhizomelic chondrodysplasia punctata type 3
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 8 of 20 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP -2.4, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- AGPS
- Protein
- p.Asn272fs
- Coding
- c.815del
- MANE Select
- NM_003659
- Type
- Deletion
- Location
- chr2:177445570 (GRCh38)
- Gene constraint
- LOEUF 0.408 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 89.27
- Residue 272
- the fad-binding pcmh-type domain
Disease context
rhizomelic chondrodysplasia punctata type 3 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Rhizomelic chondrodysplasia punctata (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Antenatal, Neonatal
- Prevalence
- 1-9 / 1 000 000 (Europe)
Similar variants
- AGPS c.563-10del Benign ★★ same condition
- AGPS c.1286delG Likely pathogenic ★ same condition
- AGPS c.557_562+5del Likely pathogenic ★ same condition
- AGPS p.Glu306fs Likely pathogenic ★ same condition
- AGPS p.Glu346fs Likely pathogenic ★ same condition
- AGPS p.Glu520fs Likely pathogenic ★ same condition
- AGPS p.Thr549del Uncertain significance same condition
- AGPS p.Arg182Ter Pathogenic/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/agps-p-asn272fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown