CCDC6 p.His154=
c.462T>C · rs150156231 · VCV709698
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.441%, 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 |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.2 | GERP 5.2, phastCons 1 |
| Overall | ||
| CADD | 8.486 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.441%
African / African-American · 330/74,886 alleles
Filtering AF
0.401%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.386%
Overall
0.0235%
378/1,611,832 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.441% | 227 |
| Remaining individualsnot grpmax-eligible | 0.0272% | 3,673 |
| Admixed American | 0.0101% | 9,939 |
| European (non-Finnish) | 0.00212% | 47,163 |
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
- CCDC6
- Protein
- p.His154=
- Coding
- c.462T>C
- MANE Select
- NM_005436
- dbSNP
- rs150156231
- Type
- single nucleotide variant
- Location
- chr10:59832645 (GRCh38)
- Gene constraint
- LOEUF 0.562 · pLI 0.89 (gnomAD)
- Structure
- AlphaFold pLDDT 76.03 · 2 PDB
- Residue 154
- the '5 x 29 aa tandem repeats' region
Similar variants
- CCDC6 p.Leu206= Benign ★★ same type
- CCDC6 p.Ala13Thr Uncertain significance ★ ⚠ same type
- CCDC6 p.Arg197Gln Uncertain significance ★ ⚠ same type
- CCDC6 p.Arg271Gln Uncertain significance ★ ⚠ same type
- CCDC6 p.Arg298Thr Uncertain significance ★ ⚠ same type
- CCDC6 p.Arg415Gln Uncertain significance ★ ⚠ same type
- CCDC6 p.Asn267Ser Uncertain significance ★ ⚠ same type
- CCDC6 p.Cys319Ser 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/ccdc6-p-his154 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown