Is COMP p.Gly299Arg (c.895G>A) pathogenic?

COMP p.Gly299Arg (c.895G>A) is classified Pathogenic/Likely pathogenic in COMP (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-10-05). AlphaMissense: likely pathogenic (0.8728); Absent from gnomAD v4.1; Associated with pseudoachondroplasia.

What condition is associated with COMP p.Gly299Arg (c.895G>A)?

COMP p.Gly299Arg (c.895G>A) is associated with pseudoachondroplasia (ClinVar).

How common is COMP p.Gly299Arg (c.895G>A) in the general population?

COMP p.Gly299Arg (c.895G>A) is absent from gnomAD v4.1 (gnomAD).

How is Pseudoachondroplasia inherited?

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

What do computational predictors say about COMP p.Gly299Arg (c.895G>A)?

AlphaMissense predicts likely pathogenic (score 0.8728) — an in-silico prediction, not a clinical call.

COMP p.Gly299Arg

c.895G>A · rs2145903238 · VCV1373104

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely pathogenic

0.8728 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

pseudoachondroplasia

Computational evidence

Protein change
AlphaMissense	0.8728	likely pathogenic ✓ concordant with ClinVar
REVEL	0.965	strongly pathogenic-leaning
SaProt	LLR -9.18	tolerated
⇒ AlphaMissense and REVEL call this damaging; SaProt does not.
Splicing
SpliceAI	Δ0.26	acceptor gain · deltas
Constraint at this position
Conservation	phyloP 7.6	GERP 2, phastCons 1
Regional constraint	o/e 0.84	unconstrained · MANE · 8,351 bp · p 2.2e-07 · regional, not allelic
Overall
CADD	33.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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: COMP
Protein: p.Gly299Arg
Coding: c.895G>A
MANE Select: NM_000095
dbSNP: rs2145903238
Type: single nucleotide variant
Location: chr19:18788292 (GRCh38)
Gene constraint: LOEUF 1.073 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 88.60 · 1 PDB
Residue 299: the 'disordered' region; a disulfide bond; a UniProt-annotated variant site (in psach)

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

Disease context

pseudoachondroplasia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Pseudoachondroplasia (Orphanet):

Inheritance: Autosomal dominant
Onset: Infancy, Neonatal
Prevalence: 1-9 / 100 000 (Worldwide)

Similar variants

COMP p.Asp269Gly Pathogenic/Likely pathogenic ★★ same condition
COMP p.Asp273Val Likely pathogenic ★★ same condition
COMP p.Asp349His Pathogenic ★★ same condition
COMP p.Asp385Asn Pathogenic/Likely pathogenic ★★ same condition
COMP p.Asp399Asn Likely pathogenic ★★ same condition
COMP p.Asp437Asn Likely pathogenic ★★ same condition
COMP p.Asp439Gly Likely pathogenic ★★ same condition
COMP p.Asp439Tyr 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/comp-p-gly299arg (accessed [today's date]).

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