CCDC168 p.Arg86=
c.258G>A · rs566704317 · VCV717318
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.52%, 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 -0.94 | GERP -3.8 |
| Overall | ||
| CADD | 0.929 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.52%
African / African-American · 1,110/73,074 alleles
Filtering AF
1.44%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.41%
Overall
0.0808%
1,250/1,547,528 alleles · low-frequency
exomes 588/1,395,340 · genomes 662/152,188 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.52% | 66 |
| Remaining individualsnot grpmax-eligible | 0.108% | 923 |
| Admixed American | 0.102% | 977 |
| Middle Eastern | 0.0668% | 1,496 |
| European (non-Finnish) | 0.00157% | 63,557 |
| South Asian | 0.0012% | 83,454 |
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
- CCDC168
- Protein
- p.Arg86=
- Coding
- c.258G>A
- MANE Select
- NM_001146197
- dbSNP
- rs566704317
- Type
- single nucleotide variant
- Location
- chr13:102758550 (GRCh38)
- Gene constraint
- LOEUF 1.661 · pLI 0.02 (gnomAD)
Similar variants
- LRTM3 p.Arg5585Ter Uncertain significance ★★ same type
- CCDC168 p.Arg2140Gln Benign ★★ same type
- CCDC168 p.Asn6517Ser Benign ★★ same type
- CCDC168 p.Cys4576Arg Benign ★★ same type
- CCDC168 p.Glu4239Lys Benign ★★ same type
- CCDC168 p.Gly1532Cys Benign ★★ same type
- CCDC168 p.Ser4840= Benign ★★ same type
- CCDC168 p.Ser5167= 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/ccdc168-p-arg86 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown