Is CTF1 p.Arg106fs (c.317del) pathogenic?

CTF1 p.Arg106fs (c.317del) is classified Uncertain significance in CTF1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-05-05). Absent from gnomAD.

How common is CTF1 p.Arg106fs (c.317del) in the general population?

CTF1 p.Arg106fs (c.317del) is absent from gnomAD (gnomAD).

CTF1 p.Arg106fs

c.317del · rs2543740551 · VCV2862171

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	escapes	premature termination codon in the last exon (3 of 3) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.8	GERP 1.3, 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: CTF1
Protein: p.Arg106fs
Coding: c.317del
MANE Select: NM_001330
dbSNP: rs2543740551
Type: Deletion
Location: chr16:30902250 (GRCh38)
Gene constraint: LOEUF 1.959 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.94

Full CTF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CTF1 p.Arg106= Likely benign ★ same residue
CTF1 p.Gln29_Thr30delinsPro Uncertain significance ★ same type
CTF1 p.Glu153fs Uncertain significance ★ same type
CTF1 p.Leu119fs Uncertain significance ★ same type
CTF1 p.Phe168del Uncertain significance ★ same type
CTF1 p.Pro116_Ala125del Uncertain significance ★ same type
CTF1 c.145-313_145-312del 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/ctf1-p-arg106fs (accessed [today's date]).

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