Is CTF1 p.Arg182= (c.546C>T) pathogenic?

CTF1 p.Arg182= (c.546C>T) is classified Uncertain significance in CTF1 (ClinVar, Single submitter, 1 submitter; last evaluated 2012-02-13). Very rare (popmax 0.00146%, afr).

How common is CTF1 p.Arg182= (c.546C>T) in the general population?

CTF1 p.Arg182= (c.546C>T) is very rare (popmax 0.00146%, afr) (gnomAD).

CTF1 p.Arg182=

c.546C>T · rs397516651 · VCV44181

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00146%, afr)

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
Pangolin	Δ0.70	gain · loss 0.00 · not in the SpliceAI release · independent
Constraint at this position
Conservation	phyloP 0.52	GERP 1.4, phastCons 0.96
Overall
CADD	9.864	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00146% African / African-American · 1/68,474 alleles

Filtering AF 0.000846% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000685%

Overall 0.00115% 17/1,479,278 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00146%	68,474
European (non-Finnish)	0.00143%	69,943

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: CTF1
Protein: p.Arg182=
Coding: c.546C>T
MANE Select: NM_001330
dbSNP: rs397516651
Type: single nucleotide variant
Location: chr16:30902479 (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.Arg182Ser Uncertain significance ★ ⚠ same residue
CTF1 c.*5C>A Uncertain significance ★★ same type
CTF1 p.Ala156Thr Uncertain significance ★★ ⚠ same type
CTF1 p.Ala34Val Uncertain significance ★★ ⚠ same type
CTF1 p.Arg107Ser Uncertain significance ★★ ⚠ same type
CTF1 p.Arg176His Uncertain significance ★★ ⚠ same type
CTF1 p.Arg65Gln Uncertain significance ★★ ⚠ same type
CTF1 p.Asp191Glu 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/ctf1-p-arg182 (accessed [today's date]).

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