Is CTF1 p.Pro116Thr (c.345_346delinsAA) pathogenic?

CTF1 p.Pro116Thr (c.345346delinsAA) is classified Uncertain significance in CTF1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-29). Absent from gnomAD.

How common is CTF1 p.Pro116Thr (c.345_346delinsAA) in the general population?

CTF1 p.Pro116Thr (c.345_346delinsAA) is absent from gnomAD (gnomAD).

CTF1 p.Pro116Thr

c.345_346delinsAA · rs1555485191 · VCV478117

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

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.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -1.3	GERP -2.5
Regional constraint	o/e 0.94	unconstrained · MANE · 5,892 bp · p 0.33 · regional, not allelic

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.Pro116Thr
Coding: c.345_346delinsAA
MANE Select: NM_001330
dbSNP: rs1555485191
Type: Indel
Location: chr16:30902278 (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.Pro116Arg Uncertain significance ★★ ⚠ same residue
CTF1 p.Pro116Leu Uncertain significance ★★ ⚠ same residue
CTF1 p.Pro116_Ala125del Uncertain significance ★ same residue
CTF1 p.Pro116Ala Uncertain significance ★ ⚠ same residue
CTF1 p.Pro116fs Uncertain significance ★ same residue

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-pro116thr (accessed [today's date]).

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