Is CFC1 p.Arg87fs (c.260_267del) pathogenic?

CFC1 p.Arg87fs (c.260267del) is classified Uncertain significance in CFC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-13). Absent from gnomAD v4.1.

How common is CFC1 p.Arg87fs (c.260_267del) in the general population?

CFC1 p.Arg87fs (c.260_267del) is absent from gnomAD v4.1 (gnomAD).

CFC1 p.Arg87fs

c.260_267del · rs1177836903 · VCV1878757

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 12,054)

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 4 of 6
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6.7	phastCons 1
Overall
CADD	33.0	PHRED · no single calibrated threshold — expert panels disagree
Region caveats
Repeat context	seg dup	· reads may not map uniquely · confidence, not pathogenicity

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 12,054). 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: CFC1
Protein: p.Arg87fs
Coding: c.260_267del
MANE Select: NM_032545
dbSNP: rs1177836903
Type: Deletion
Location: chr2:130597963 (GRCh38)
Gene constraint: LOEUF 0.586 · pLI 0.86 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 64.18
Residue 87: the egf-like domain

Full CFC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFC1 p.Ala175fs Conflicting classifications of pathogenicity ★ same type
CFC1 p.Lys30fs Uncertain significance ★ same type
CFC1 p.Pro217fs Uncertain significance ★ 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/cfc1-p-arg87fs (accessed [today's date]).

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