Is COL11A1 p.Ser55fs (c.162del) pathogenic?

COL11A1 p.Ser55fs (c.162del) is classified Likely pathogenic in COL11A1 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-11-08). Absent from gnomAD.

How common is COL11A1 p.Ser55fs (c.162del) in the general population?

COL11A1 p.Ser55fs (c.162del) is absent from gnomAD (gnomAD).

COL11A1 p.Ser55fs

c.162del · rs1571238944 · VCV817893

Likely pathogenic Single submitter

Classification

Likely 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 in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 2 of 67
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 5.1	GERP -1, 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: COL11A1
Protein: p.Ser55fs
Coding: c.162del
MANE Select: NM_001854
dbSNP: rs1571238944
Type: Deletion
Location: chr1:103082917 (GRCh38)
Gene constraint: LOEUF 0.349 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 53.06

Full COL11A1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

COL11A1 c.1630-2del Pathogenic ★★ same type
COL11A1 c.2796_2813delTCAAGGACCTCAGGGTCC Pathogenic ★★ same type
COL11A1 p.Asn398fs Pathogenic ★★ same type
COL11A1 p.Gly1240fs Pathogenic/Likely pathogenic ★★ same type
COL11A1 c.1792-10_1792-8del Likely benign ★★ same type
COL11A1 c.2143-10del Benign/Likely benign ★★ same type
COL11A1 c.2340+9_2340+13del Benign/Likely benign ★★ same type
COL11A1 c.2502+16del Likely benign ★★ 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/col11a1-p-ser55fs (accessed [today's date]).

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