ORC6 p.Arg137=
c.411G>A · rs1216183499 · VCV1940717
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00534%, afr)
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 5.8 | GERP 3.8, phastCons 1 |
| Overall | ||
| CADD | 12.55 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00534%
African / African-American · 4/74,902 alleles
Filtering AF
0.00175%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.000248%
4/1,613,218 alleles · very rare
exomes 1/1,461,052 · genomes 3/152,166 · joint denominator
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
- ORC6
- Protein
- p.Arg137=
- Coding
- c.411G>A
- MANE Select
- NM_014321
- dbSNP
- rs1216183499
- Type
- single nucleotide variant
- Location
- chr16:46693144 (GRCh38)
- Gene constraint
- LOEUF 1.784 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 81.69 · 4 PDB
Similar variants
- ORC6 p.Arg137Gly Uncertain significance ★ ⚠ same residue
- ORC6 p.Ala10Ser Uncertain significance ★★ ⚠ same type
- ORC6 p.Arg8His Uncertain significance ★★ ⚠ same type
- ORC6 p.Arg8Leu Uncertain significance ★★ ⚠ same type
- ORC6 p.Gln130His Uncertain significance ★★ ⚠ same type
- ORC6 p.Ile69Met Uncertain significance ★★ ⚠ same type
- ORC6 p.Leu228Val Uncertain significance ★★ ⚠ same type
- ORC6 p.Leu92Pro 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/orc6-p-arg137 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown