Is CCNF p.Arg248fs (c.742_743del) pathogenic?

CCNF p.Arg248fs (c.742743del) is classified Uncertain significance in CCNF (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-01). Absent from gnomAD.

How common is CCNF p.Arg248fs (c.742_743del) in the general population?

CCNF p.Arg248fs (c.742_743del) is absent from gnomAD (gnomAD).

CCNF p.Arg248fs

c.742_743del · rs2505757908 · VCV3026850

Uncertain significance Single submitter

Classification

Uncertain significance

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 8 of 17
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 5.9	GERP 1.8, 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: CCNF
Protein: p.Arg248fs
Coding: c.742_743del
MANE Select: NM_001761
dbSNP: rs2505757908
Type: Deletion
Location: chr16:2439791 (GRCh38)
Gene constraint: LOEUF 0.531 · pLI 0.70 (gnomAD)
Structure: AlphaFold pLDDT 72.34 · 1 PDB
Residue 248: an α-helix

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

Similar variants

CCNF c.595-8_595-5del Uncertain significance ★ same type
CCNF c.279-140_279-123del Benign ★ same type
CCNF c.279-140_279-125del Benign ★ same type
CCNF c.279-142_279-123del Benign ★ same type
CCNF c.279-142_279-129del Benign ★ same type
CCNF c.279-178_279-161del 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/ccnf-p-arg248fs (accessed [today's date]).

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