COLEC10 p.Pro72=
c.216G>A · rs116835812 · VCV783530
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.23%, 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 -14 | GERP -5.2 |
| Overall | ||
| CADD | 0.086 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.23%
African / African-American · 1,669/74,992 alleles
Filtering AF
2.14%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.1%
Overall
0.114%
1,834/1,612,090 alleles · low-frequency
exomes 915/1,459,792 · genomes 919/152,298 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.23% | 45 |
| Remaining individualsnot grpmax-eligible | 0.112% | 891 |
| Admixed American | 0.0967% | 1,034 |
| Middle Eastern | 0.033% | 3,027 |
| South Asian | 0.00659% | 15,170 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,598 |
| European (non-Finnish) | 0.00238% | 42,085 |
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
- COLEC10
- Protein
- p.Pro72=
- Coding
- c.216G>A
- MANE Select
- NM_006438
- dbSNP
- rs116835812
- Type
- single nucleotide variant
- Location
- chr8:119089747 (GRCh38)
- Gene constraint
- LOEUF 1.082 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.20
- Residue 72
- the collagen-like domain; the 'disordered' region; a UniProt-annotated variant site (in 3mc3; results in lack of protein)
Similar variants
- COLEC10 p.Pro72Leu Uncertain significance ★ ⚠ same residue
- COLEC10 p.Arg9Ter Pathogenic ★★ same type
- COLEC10 c.346+5G>A Benign ★★ same type
- COLEC10 c.442+1G>A Likely pathogenic ★ same type
- COLEC10 p.Gly104Val Likely pathogenic ★ same type
- COLEC10 c.149-7945A>C Uncertain significance ★ same type
- COLEC10 p.Ala184Pro Uncertain significance ★ ⚠ same type
- COLEC10 p.Ala5Glu 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/colec10-p-pro72 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown