Is CFAP276 p.Arg160Ter (c.478C>T) pathogenic?

CFAP276 p.Arg160Ter (c.478C>T) is classified Uncertain significance in CFAP276 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-08). Very rare (popmax 0.00492%, nfe).

How common is CFAP276 p.Arg160Ter (c.478C>T) in the general population?

CFAP276 p.Arg160Ter (c.478C>T) is very rare (popmax 0.00492%, nfe) (gnomAD).

CFAP276 p.Arg160Ter

c.478C>T · VCV4879333

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00492%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (5 of 5) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.7	GERP 1, phastCons 1
Overall
CADD	38.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00492% European (non-Finnish) · 58/1,179,826 alleles

Filtering AF 0.00386% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00353%

Overall 0.00397% 64/1,613,592 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00492%	20,342
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,600
Admixed American	0.00334%	29,983
South Asian	0.0022%	45,495
Remaining individualsnot grpmax-eligible	0.0016%	62,476

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: CFAP276
Protein: p.Arg160Ter
Coding: c.478C>T
MANE Select: NM_001245025
Type: single nucleotide variant
Location: chr1:109106060 (GRCh38)
Structure: AlphaFold pLDDT 67.55 · 2 PDB
Residue 160: the 'disordered' region

Full CFAP276 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP276 p.Arg10Ser Uncertain significance ★ same type
CFAP276 p.Arg46Gln Uncertain significance ★ ⚠ same type
CFAP276 p.Gln143Glu Uncertain significance ★ ⚠ same type
CFAP276 c.45+725G>T Likely benign ★ same type
CFAP276 p.Ile122Asn Uncertain significance ⚠ same type
CFAP276 p.Lys28Ile 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/cfap276-p-arg160ter (accessed [today's date]).

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