Is AGPS c.1286delG pathogenic?

AGPS c.1286delG is classified Likely pathogenic in AGPS (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-21). Associated with rhizomelic chondrodysplasia punctata type 3.

What condition is associated with AGPS c.1286delG?

AGPS c.1286delG is associated with rhizomelic chondrodysplasia punctata type 3 (ClinVar).

How is Rhizomelic chondrodysplasia punctata inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

AGPS c.1286delG

VCV4815255

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

Conditions

rhizomelic chondrodysplasia punctata type 3

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	GERP 1.8, phastCons 1
Non-coding constraint	Z 2.99	1 kb window · o/e 0.77 · regional · uncalibrated

Variant & gene context

Gene: AGPS
Coding: c.1286delG
MANE Select: NM_003659
Type: Deletion
Location: chr2:177497688 (GRCh38)
Gene constraint: LOEUF 0.408 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 89.27

Full AGPS gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

rhizomelic chondrodysplasia punctata type 3 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For 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.557_562+5del Likely pathogenic ★ same condition
AGPS p.Asn272fs 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-c-1286delg (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown