MORC2 p.Pro479=
c.1437A>G · rs3747151 · VCV1168329
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Common
common (popmax 63.2%, eas) — too common for a highly-penetrant pathogenic allele
Conditions
2
developmental delay, impaired growth, dysmorphic facies, and axonal neuropathy
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 -2.2 | GERP -3.2 |
| Overall | ||
| CADD | 8.755 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
63.2%
East Asian · 28,359/44,856 alleles
Filtering AF
62.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 62.4%
Overall
33.7%
543,326/1,613,566 alleles · common
exomes 482,974/1,461,598 · genomes 60,352/151,968 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 63.2% | 2 |
| African / African-American | 55.4% | 2 |
| Remaining individualsnot grpmax-eligible | 35.3% | 3 |
| Ashkenazi Jewishnot grpmax-eligible | 33.3% | 3 |
| Finnishnot grpmax-eligible | 32.2% | 3 |
| Admixed American | 32% | 3 |
| European (non-Finnish) | 31.6% | 3 |
| Middle Eastern | 30.9% | 3 |
| South Asian | 29.5% | 3 |
| Amishnot grpmax-eligible | 29.3% | 3 |
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.Pro479=
- Coding
- c.1437A>G
- MANE Select
- NM_001303256
- dbSNP
- rs3747151
- Type
- single nucleotide variant
- Location
- chr22:30937644 (GRCh38)
- Gene constraint
- LOEUF 0.3 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 78.37 · 9 PDB
- Residue 479
- an α-helix
Similar variants
- MORC2 p.Arg132Cys Pathogenic/Likely pathogenic ★★ same condition
- MORC2 p.Arg132His Pathogenic/Likely pathogenic ★★ ⚠ same condition
- MORC2 p.Arg252Trp Pathogenic/Likely pathogenic ★★ same condition
- MORC2 p.Arg266Ser Pathogenic/Likely pathogenic ★★ same condition
- MORC2 p.Asp466Asn Pathogenic/Likely pathogenic ★★ ⚠ same condition
- MORC2 p.Glu236Gly Pathogenic/Likely pathogenic ★★ same condition
- MORC2 p.Glu27Lys Pathogenic/Likely pathogenic ★★ ⚠ same condition
- MORC2 p.Ser87Leu 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/morc2-p-pro479 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown