Is CCNF p.Arg349= (c.1047G>T) pathogenic?

CCNF p.Arg349= (c.1047G>T) is classified Likely benign in CCNF (ClinVar, No assertion criteria, 1 submitter; last evaluated 2020-02-10). Ultra-rare (popmax 0.0157%, nfe); Associated with CCNF-related disorder.

What condition is associated with CCNF p.Arg349= (c.1047G>T)?

CCNF p.Arg349= (c.1047G>T) is associated with CCNF-related disorder (ClinVar).

How common is CCNF p.Arg349= (c.1047G>T) in the general population?

CCNF p.Arg349= (c.1047G>T) is ultra-rare (popmax 0.0157%, nfe) (gnomAD).

CCNF p.Arg349=

c.1047G>T · rs144631476 · VCV3051951

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0157%, nfe)

Conditions

CCNF-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.094	GERP -3.1, phastCons 0.62
Overall
CADD	3.329	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0157% European (non-Finnish) · 185/1,180,018 alleles

Filtering AF 0.0138% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0131%

Overall 0.0121% 196/1,613,820 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0157%	6,378
African / African-American	0.00666%	15,008
Remaining individualsnot grpmax-eligible	0.0064%	15,621
Finnishnot grpmax-eligible	0.00313%	31,912

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: CCNF
Protein: p.Arg349=
Coding: c.1047G>T
MANE Select: NM_001761
dbSNP: rs144631476
Type: single nucleotide variant
Location: chr16:2445575 (GRCh38)
Gene constraint: LOEUF 0.531 · pLI 0.70 (gnomAD)
Structure: AlphaFold pLDDT 72.34 · 1 PDB
Residue 349: the cyclin n-terminal domain; an α-helix

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

Disease context

CCNF-related disorder

Similar variants

CCNF p.Arg349Gln Uncertain significance ★ ⚠ same residue
CCNF c.347-4G>A Likely benign same condition
CCNF p.Ala145= Likely benign same condition
CCNF p.Ala74Thr Benign same condition
CCNF p.Leu352= Likely benign same condition
CCNF p.Leu531Arg Likely benign ⚠ same condition
CCNF p.Ser704= Likely benign same condition
CCNF p.Tyr250= Likely benign same condition

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-arg349 (accessed [today's date]).

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