Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Common
common (popmax 9.34%, mid) — too common for a highly-penetrant pathogenic allele
Conditions
1
Compton-North congenital myopathy
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 -8 | GERP -3.5 |
| Overall | ||
| CADD | 0.451 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
9.34%
Middle Eastern · 477/5,108 alleles
Filtering AF
8.65%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 8.37%
Overall
4.14%
66,708/1,612,264 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 9.34% | 11 |
| Amishnot grpmax-eligible | 8.55% | 12 |
| South Asian | 5.61% | 18 |
| Ashkenazi Jewishnot grpmax-eligible | 4.96% | 20 |
| Admixed American | 4.8% | 21 |
| European (non-Finnish) | 4.41% | 23 |
| Remaining individualsnot grpmax-eligible | 3.99% | 25 |
| Finnishnot grpmax-eligible | 2.07% | 48 |
| African / African-American | 0.833% | 120 |
| East Asian | 0.555% | 180 |
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
- CNTN1
- Protein
- p.Ala652=
- Coding
- c.1956A>G
- MANE Select
- NM_001843
- dbSNP
- rs2229930
- Type
- single nucleotide variant
- Location
- chr12:40981060 (GRCh38)
- Gene constraint
- LOEUF 0.431 · pLI 1.00 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 87.29 · 2 PDB
- Residue 652
- the fibronectin type-iii 1 domain
Disease context
Compton-North congenital myopathy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Congenital lethal myopathy, Compton-North type (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Antenatal, Neonatal
Similar variants
- CNTN1 p.Ala410Val Uncertain significance ★★ ⚠ same condition
- CNTN1 p.Ala514Thr Uncertain significance ★★ ⚠ same condition
- CNTN1 p.Ala528Val Uncertain significance ★★ ⚠ same condition
- CNTN1 p.Ala668Thr Uncertain significance ★★ ⚠ same condition
- CNTN1 p.Ala799Thr Uncertain significance ★★ ⚠ same condition
- CNTN1 p.Ala930Ser Uncertain significance ★★ ⚠ same condition
- CNTN1 p.Ala995Thr Uncertain significance ★★ ⚠ same condition
- CNTN1 p.Arg274Gln Uncertain significance ★★ ⚠ 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/cntn1-p-ala652 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown