CCDC174 p.Arg366=
c.1098C>T · rs139954564 · VCV715841
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.116%, mid)
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 -1.3 | GERP -5.3 |
| Overall | ||
| CADD | 5.444 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.116%
Middle Eastern · 7/6,046 alleles
Filtering AF
0.0543%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0385%
Overall
0.0165%
266/1,608,594 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.116% | 864 |
| European (non-Finnish) | 0.0195% | 5,124 |
| Remaining individualsnot grpmax-eligible | 0.0161% | 6,225 |
| African / African-American | 0.0094% | 10,643 |
| Admixed American | 0.00857% | 11,665 |
| South Asian | 0.00555% | 18,009 |
| East Asian | 0.00447% | 22,347 |
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
- CCDC174
- Protein
- p.Arg366=
- Coding
- c.1098C>T
- MANE Select
- NM_016474
- dbSNP
- rs139954564
- Type
- single nucleotide variant
- Location
- chr3:14670079 (GRCh38)
- Gene constraint
- LOEUF 0.926 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.79
Similar variants
- CCDC174 p.Arg366Cys Uncertain significance ★ ⚠ same residue
- CCDC174 p.Arg366His Uncertain significance ★ ⚠ same residue
- CCDC174 p.Asp395His Uncertain significance ★★ ⚠ same type
- CCDC174 p.Phe29Ser Uncertain significance ★★ ⚠ same type
- CCDC174 p.Pro158Ser Uncertain significance ★★ ⚠ same type
- CCDC174 c.1106-10T>A Benign/Likely benign ★★ same type
- CCDC174 c.308-55C>A Benign ★★ same type
- CCDC174 c.485+47G>A 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/ccdc174-p-arg366 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown