MORC2 p.Ala32=
c.96C>T · rs737924 · VCV1164340
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Common
common (popmax 62.8%, 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 | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.5 | GERP -2.7, phastCons 1 |
| Overall | ||
| CADD | 9.828 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
62.8%
East Asian · 25,616/40,796 alleles
Filtering AF
62.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 61.9%
Overall
34.4%
530,674/1,544,876 alleles · common
exomes 469,132/1,393,084 · genomes 61,542/151,792 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 62.8% | 2 |
| African / African-American | 56.8% | 2 |
| Remaining individualsnot grpmax-eligible | 36.1% | 3 |
| Ashkenazi Jewishnot grpmax-eligible | 33.6% | 3 |
| Admixed American | 32.9% | 3 |
| Middle Eastern | 32.7% | 3 |
| Finnishnot grpmax-eligible | 32.6% | 3 |
| European (non-Finnish) | 32.3% | 3 |
| South Asian | 30.3% | 3 |
| Amishnot grpmax-eligible | 29.6% | 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.Ala32=
- Coding
- c.96C>T
- MANE Select
- NM_001303256
- dbSNP
- rs737924
- Type
- single nucleotide variant
- Location
- chr22:30958667 (GRCh38)
- Gene constraint
- LOEUF 0.3 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 78.37 · 9 PDB
- Residue 32
- an α-helix
Similar variants
- MORC2 p.Ala32Gly Uncertain significance ★ same residue
- 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
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-ala32 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown