CCDC174 p.Leu183=
c.549G>T · rs151323660 · VCV736523
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0295%, nfe)
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 1.1 | GERP 1.6, phastCons 0.99 |
| Overall | ||
| CADD | 6.739 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0295%
European (non-Finnish) · 348/1,179,858 alleles
Filtering AF
0.0269%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0259%
Overall
0.0228%
368/1,614,002 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0295% | 3,390 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,209 |
| Middle Eastern | 0.0165% | 6,062 |
| African / African-American | 0.004% | 25,015 |
| Admixed American | 0.00333% | 30,012 |
| Finnishnot grpmax-eligible | 0.00312% | 32,014 |
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.Leu183=
- Coding
- c.549G>T
- MANE Select
- NM_016474
- dbSNP
- rs151323660
- Type
- single nucleotide variant
- Location
- chr3:14665091 (GRCh38)
- Gene constraint
- LOEUF 0.926 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.79
Similar variants
- 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
- CCDC174 c.485+83C>G Benign ★★ same type
- CCDC174 c.485+83C>T 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-leu183 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown