Is COL1A2 c.-287C>T pathogenic?

COL1A2 c.-287C>T is classified Benign/Likely benign in COL1A2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2018-06-27). Low-frequency (popmax 2.38%, mid); Associated with Ehlers-Danlos syndrome, arthrochalasia type, 2.

What condition is associated with COL1A2 c.-287C>T?

COL1A2 c.-287C>T is associated with Ehlers-Danlos syndrome, arthrochalasia type, 2, osteogenesis imperfecta (ClinVar).

How common is COL1A2 c.-287C>T in the general population?

COL1A2 c.-287C>T is low-frequency (popmax 2.38%, mid) (gnomAD).

How is Arthrochalasia Ehlers-Danlos syndrome inherited?

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

COL1A2 c.-287C>T

rs190926256 · VCV360939

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

low-frequency (popmax 2.38%, mid)

Conditions

Ehlers-Danlos syndrome, arthrochalasia type, 2

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 3.9	GERP 1.8, phastCons 1
Non-coding constraint	Z 2.33	1 kb window · o/e 0.85 · regional · uncalibrated
Overall
CADD	19.03	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.38% Middle Eastern · 39/1,638 alleles

Filtering AF 1.79% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.58%

Overall 1.06% 4,976/469,744 alleles · low-frequency

Ancestry group	Frequency	1 in
Middle Easterngrpmax	2.38%	42
Ashkenazi Jewishnot grpmax-eligible	1.89%	53
European (non-Finnish)	1.46%	69
Remaining individualsnot grpmax-eligible	1.32%	76
Admixed American	1.04%	97
Finnishnot grpmax-eligible	0.428%	234
South Asian	0.309%	324
African / African-American	0.242%	413
Amishnot grpmax-eligible	0.11%	912

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: COL1A2
Coding: c.-287C>T
MANE Select: NM_000089
dbSNP: rs190926256
Type: single nucleotide variant
Location: chr7:94394745 (GRCh38)
Gene constraint: LOEUF 0.339 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 55.02 · 5 PDB

Full COL1A2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Ehlers-Danlos syndrome, arthrochalasia type, 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: osteogenesis imperfecta

For Arthrochalasia Ehlers-Danlos syndrome (Orphanet):

Inheritance: Autosomal dominant
Onset: Infancy, Neonatal

Similar variants

COL1A2 c.1503+1G>A Pathogenic/Likely pathogenic ★★ same condition
COL1A2 c.226-2A>G Pathogenic/Likely pathogenic ★★ same condition
COL1A2 c.433-2A>C Pathogenic/Likely pathogenic ★★ same condition
COL1A2 c.433-2A>G Pathogenic/Likely pathogenic ★★ same condition
COL1A2 c.595-2A>G Pathogenic/Likely pathogenic ★★ same condition
COL1A2 p.Cys1195Arg Pathogenic/Likely pathogenic ★★ same condition
COL1A2 p.Gly1012Ser Pathogenic/Likely pathogenic ★★ same condition
COL1A2 p.Gly1024Arg 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/col1a2-c-minus-287c-t (accessed [today's date]).

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