DHCR7 p.Ile245=
c.735C>A · rs12800 · VCV1087179
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Conditions
1
Smith-Lemli-Opitz syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.321 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -3.4 | GERP -3.5 |
| Overall | ||
| CADD | 0.656 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,872 alleles
Overall
6.84e-05%
1/1,461,720 alleles · very rare
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
- DHCR7
- Protein
- p.Ile245=
- Coding
- c.735C>A
- MANE Select
- NM_001360
- dbSNP
- rs12800
- Type
- single nucleotide variant
- Location
- chr11:71438975 (GRCh38)
- Gene constraint
- LOEUF 1.087 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.64
Similar variants
- DHCR7 c.322-1G>A Likely pathogenic ★★ same condition
- DHCR7 c.412+3A>T Likely pathogenic ★★ same condition
- DHCR7 c.413-2A>G Likely pathogenic ★★ same condition
- DHCR7 c.626+1G>A Likely pathogenic ★★ same condition
- DHCR7 c.626+1G>T Likely pathogenic ★★ same condition
- DHCR7 c.627-1G>A Likely pathogenic ★★ same condition
- DHCR7 c.831+1G>T Pathogenic/Likely pathogenic ★★ same condition
- DHCR7 c.831+2T>A Pathogenic/Likely pathogenic ★★ same condition
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/dhcr7-p-ile245 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown