Is COL1A1 p.Gly485= (c.1455C>T) pathogenic?

COL1A1 p.Gly485= (c.1455C>T) is classified Likely benign in COL1A1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-25). Very rare (popmax 0.00479%, eas); Associated with osteogenesis imperfecta type 1.

What condition is associated with COL1A1 p.Gly485= (c.1455C>T)?

COL1A1 p.Gly485= (c.1455C>T) is associated with osteogenesis imperfecta type 1 (ClinVar).

How common is COL1A1 p.Gly485= (c.1455C>T) in the general population?

COL1A1 p.Gly485= (c.1455C>T) is very rare (popmax 0.00479%, eas) (gnomAD).

COL1A1 p.Gly485=

c.1455C>T · rs368476268 · VCV2110285

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00479%, eas)

Conditions

osteogenesis imperfecta type 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.96	donor gain · deltas
Pangolin	Δ0.48	gain · loss 0.03 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 1.5	GERP -2, phastCons 1
Overall
CADD	24.4	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00479% East Asian · 2/41,776 alleles

Filtering AF 0.00176% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00152%

Overall 0.00223% 35/1,567,260 alleles · very rare exomes 28/1,415,130 · genomes 7/152,130 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00479%	20,888
South Asian	0.00349%	28,685
Ashkenazi Jewishnot grpmax-eligible	0.00347%	28,838
European (non-Finnish)	0.00251%	39,847

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: COL1A1
Protein: p.Gly485=
Coding: c.1455C>T
MANE Select: NM_000088
dbSNP: rs368476268
Type: single nucleotide variant
Location: chr17:50194727 (GRCh38)
Gene constraint: LOEUF 0.159 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 54.26 · 14 PDB
Residue 485: the 'disordered' region; the 'triple-helical region' region

Full COL1A1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

osteogenesis imperfecta type 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

COL1A1 p.Gly485Ala Pathogenic ★ same residue
COL1A1 p.Gly485Ser Likely pathogenic ★ same residue
COL1A1 p.Gly485fs Pathogenic ★ same residue
COL1A1 c.1003-1G>A Pathogenic/Likely pathogenic ★★ same condition
COL1A1 c.103+1G>A Pathogenic/Likely pathogenic ★★ same condition
COL1A1 c.103+2T>C Pathogenic ★★ same condition
COL1A1 c.104-1G>T Pathogenic/Likely pathogenic ★★ same condition
COL1A1 c.104-2A>G 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/col1a1-p-gly485 (accessed [today's date]).

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