SHH p.Pro220=
c.660C>T · VCV4898700
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,598,224)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.31 | GERP -2.9, phastCons 0.98 |
| Overall | ||
| CADD | 9.401 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,598,224). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- SHH
- Protein
- p.Pro220=
- Coding
- c.660C>T
- MANE Select
- NM_000193
- Type
- single nucleotide variant
- Location
- chr7:155803629 (GRCh38)
- Gene constraint
- LOEUF 0.493 · pLI 0.98 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 80.23 · 20 PDB
Similar variants
- SHH c.562+1G>A Pathogenic ★★ same type
- SHH p.Arg72Ter Pathogenic ★★ same type
- SHH p.Asp222Asn Likely pathogenic ★★ same type
- SHH p.Cys198Arg Pathogenic/Likely pathogenic ★★ same type
- SHH p.Cys198Ser Likely pathogenic ★★ same type
- SHH p.Leu266Phe Likely pathogenic ★★ same type
- SHH p.Leu271Pro Likely pathogenic ★★ same type
- SHH p.Pro347Arg Likely pathogenic ★★ 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/shh-p-pro220 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown