CLIC6 p.Ser550=
c.1650C>T · rs61733872 · VCV741218
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.7%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.42 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -6.7 | GERP -3.8 |
| Overall | ||
| CADD | 0.366 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.7%
African / African-American · 525/75,020 alleles
Filtering AF
0.65%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.631%
Overall
0.05%
807/1,614,100 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.7% | 143 |
| Middle Eastern | 0.0825% | 1,212 |
| Remaining individualsnot grpmax-eligible | 0.064% | 1,563 |
| South Asian | 0.0604% | 1,656 |
| Admixed American | 0.0467% | 2,144 |
| European (non-Finnish) | 0.0129% | 7,763 |
| East Asian | 0.00446% | 22,441 |
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
- CLIC6
- Protein
- p.Ser550=
- Coding
- c.1650C>T
- MANE Select
- NM_053277
- dbSNP
- rs61733872
- Type
- single nucleotide variant
- Location
- chr21:34708739 (GRCh38)
- Gene constraint
- LOEUF 1.445 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.24
Similar variants
- CLIC6 p.Arg436Pro Benign ★★ same type
- CLIC6 p.Arg640Lys Benign ★★ same type
- CLIC6 p.Asp616= Benign ★★ same type
- CLIC6 p.Glu401= Likely benign ★★ same type
- CLIC6 p.Ile651Val Benign ★★ same type
- CLIC6 p.Thr667= Benign ★★ same type
- CLIC6 p.Val180Leu Benign ★★ ⚠ same type
- CLIC6 p.Ala11Val 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/clic6-p-ser550 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown