MORC2 p.Glu467=
c.1401G>A · rs1420591465 · VCV3027016
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
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 -0.33 | GERP -3, phastCons 0.1 |
| Overall | ||
| CADD | 6.677 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,028 alleles
Filtering AF
6.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000248%
4/1,614,154 alleles · very rare
exomes 4/1,461,856 · genomes 0/152,298 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 60,028 |
| European (non-Finnish) | 0.000254% | 393,346 |
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
- MORC2
- Protein
- p.Glu467=
- Coding
- c.1401G>A
- MANE Select
- NM_001303256
- dbSNP
- rs1420591465
- Type
- single nucleotide variant
- Location
- chr22:30937680 (GRCh38)
- Gene constraint
- LOEUF 0.3 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 78.37 · 9 PDB
- Residue 467
- an α-helix
Similar variants
- MORC2 p.Arg132Cys Pathogenic/Likely pathogenic ★★ same type
- MORC2 p.Arg132His Pathogenic/Likely pathogenic ★★ ⚠ same type
- MORC2 p.Arg252Trp Pathogenic/Likely pathogenic ★★ same type
- MORC2 p.Arg266Ser Pathogenic/Likely pathogenic ★★ same type
- MORC2 p.Asp466Asn Pathogenic/Likely pathogenic ★★ ⚠ same type
- MORC2 p.Glu236Gly Pathogenic/Likely pathogenic ★★ same type
- MORC2 p.Glu27Lys Pathogenic/Likely pathogenic ★★ ⚠ same type
- MORC2 p.Ser87Leu 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/morc2-p-glu467 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown