Is COL18A1 p.Pro1009= (c.3027C>T) pathogenic?

COL18A1 p.Pro1009= (c.3027C>T) is classified Likely benign in COL18A1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-11-18). Ultra-rare (popmax 0.0188%, mid).

How common is COL18A1 p.Pro1009= (c.3027C>T) in the general population?

COL18A1 p.Pro1009= (c.3027C>T) is ultra-rare (popmax 0.0188%, mid) (gnomAD).

COL18A1 p.Pro1009=

c.3027C>T · rs745596998 · VCV1584141

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0188%, mid)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.131	moderately benign-leaning
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -8	GERP -2.2
Overall
CADD	0.191	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0188% Middle Eastern · 1/5,332 alleles

Filtering AF 0.00612% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00565%

Overall 0.00634% 101/1,593,252 alleles · ultra-rare exomes 97/1,441,122 · genomes 4/152,130 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0188%	5,332
South Asian	0.00886%	11,289
European (non-Finnish)	0.00739%	13,535
African / African-American	0.00671%	14,908
Remaining individualsnot grpmax-eligible	0.00162%	61,670

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: COL18A1
Protein: p.Pro1009=
Coding: c.3027C>T
MANE Select: NM_001379500
dbSNP: rs745596998
Type: single nucleotide variant
Location: chr21:45505371 (GRCh38)

Full COL18A1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/col18a1-p-pro1009 (accessed [today's date]).

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