Is COL18A1 p.Phe489fs (c.1467_1470del) pathogenic?

COL18A1 p.Phe489fs (c.14671470del) is classified Pathogenic in COL18A1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-11). No gnomAD frequency available for this variant.

How common is COL18A1 p.Phe489fs (c.1467_1470del) in the general population?

COL18A1 p.Phe489fs (c.1467_1470del) is no gnomAD frequency available for this variant (gnomAD).

COL18A1 p.Phe489fs

c.1467_1470del · rs2517627198 · VCV2855181

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 13 of 42
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.7	GERP 0.86, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: COL18A1
Protein: p.Phe489fs
Coding: c.1467_1470del
MANE Select: NM_001379500
dbSNP: rs2517627198
Type: Deletion
Location: chr21:45480713 (GRCh38)
Gene constraint: LOEUF 1.001 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 51.77 · 9 PDB
Residue 489: the laminin g-like domain

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

Similar variants

COL18A1 p.Phe489= Likely benign ★ same residue
COL18A1 p.Ala783fs Pathogenic ★★ same type
COL18A1 p.Gly387fs Pathogenic ★★ same type
COL18A1 p.Gly942fs Pathogenic/Likely pathogenic ★★ same type
COL18A1 p.Ile1182fs Pathogenic/Likely pathogenic ★★ same type
COL18A1 p.Pro1012fs Pathogenic ★★ same type
COL18A1 p.Pro1015fs Pathogenic/Likely pathogenic ★★ same type
COL18A1 p.Pro314fs Pathogenic/Likely pathogenic ★★ same type

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-phe489fs (accessed [today's date]).

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