VCAN p.Ser2572=
c.7716G>A · rs199683750 · VCV1096411
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 | GERP -1.1, phastCons 1 |
| Overall | ||
| CADD | 11.49 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,062 alleles
Filtering AF
0.00435%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00276%
Overall
0.00198%
32/1,613,746 alleles · ultra-rare
exomes 25/1,461,660 · genomes 7/152,086 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,062 |
| East Asian | 0.0112% | 8,966 |
| African / African-American | 0.00667% | 14,990 |
| South Asian | 0.00549% | 18,210 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,249 |
| Admixed American | 0.00167% | 59,970 |
| European (non-Finnish) | 0.0011% | 90,763 |
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
- VCAN
- Protein
- p.Ser2572=
- Coding
- c.7716G>A
- MANE Select
- NM_004385
- dbSNP
- rs199683750
- Type
- single nucleotide variant
- Location
- chr5:83540719 (GRCh38)
- Gene constraint
- LOEUF 0.223 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Residue 2572
- the 'gag-beta' region
Similar variants
- VCAN p.Ser2572Leu Benign/Likely benign ★★ same residue
- VCAN c.4004-1G>A Pathogenic ★★ same type
- VCAN c.4004-2A>C Pathogenic ★★ same type
- VCAN c.4004-2A>G Pathogenic ★★ same type
- VCAN c.4004-5T>C Pathogenic ★★ same type
- VCAN c.9265+1G>C Pathogenic ★★ same type
- VCAN c.9266-5G>A Uncertain significance ★★ same type
- VCAN c.9493+5G>A 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/vcan-p-ser2572 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown