Is AGPS c.*1880A>G pathogenic?

AGPS c.1880A>G is classified Uncertain significance in AGPS (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-13). Common (popmax 52%, sas) — too common for a highly-penetrant pathogenic allele; Associated with rhizomelic chondrodysplasia punctata type 3.

What condition is associated with AGPS c.*1880A>G?

AGPS c.*1880A>G 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.*1880A>G

Q: How common is AGPS c.*1880A>G in the general population?

AGPS c.*1880A>G is common (popmax 52%, sas) — too common for a highly-penetrant pathogenic allele (gnomAD).

rs58369399 · VCV893966

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 52%, sas) — too common for a highly-penetrant pathogenic allele

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 · no allele here is in the release
Constraint at this position
Conservation	phyloP -5.7	GERP -0.69
Non-coding constraint	Z 1.32	1 kb window · o/e 0.89 · regional · uncalibrated
Overall
CADD	0.597	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 52% South Asian · 344/662 alleles

Filtering AF 47.4% ClinGen BA1/BS1 input FAF95, joint · FAF99 45.7%

Overall 45.6% 5,939/13,024 alleles · common

Ancestry group	Frequency	1 in
South Asiangrpmax	52%	2
East Asian	51.5%	2
Amishnot grpmax-eligible	50%	2
Admixed American	47.6%	2
Ashkenazi Jewishnot grpmax-eligible	46.5%	2
Remaining individualsnot grpmax-eligible	45.4%	2
African / African-American	45.2%	2
Finnishnot grpmax-eligible	44.4%	2
European (non-Finnish)	44.2%	2
Middle Eastern	41.7%	2

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: AGPS
Coding: c.*1880A>G
MANE Select: NM_003659
dbSNP: rs58369399
Type: single nucleotide variant
Location: chr2:177540075 (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 p.Arg182Ter Pathogenic/Likely pathogenic ★★ same condition
AGPS p.Thr309Ile Likely pathogenic ★★ same condition
AGPS c.1855+6C>A Uncertain significance ★★ same condition
AGPS c.*118A>G Uncertain significance ★★ same condition
AGPS p.Asp28Val Uncertain significance ★★ ⚠ same condition
AGPS p.Pro415Leu Uncertain significance ★★ ⚠ same condition
AGPS p.Thr72Ala Uncertain significance ★★ ⚠ same condition
AGPS c.1233+14T>A Benign/Likely benign ★★ 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-star-1880a-g (accessed [today's date]).

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