CNTN3 p.Ser243=
c.729G>A · rs776282929 · VCV743184
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00403%, afr)
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 -2.8 | GERP -5.2 |
| Overall | ||
| CADD | 5.23 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00403%
African / African-American · 3/74,518 alleles
Filtering AF
0.00107%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00054%
Overall
0.00131%
21/1,607,706 alleles · very rare
exomes 15/1,455,670 · genomes 6/152,036 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00403% | 24,839 |
| East Asian | 0.00224% | 44,562 |
| Admixed American | 0.00169% | 59,262 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,166 |
| European (non-Finnish) | 0.00119% | 84,011 |
| South Asian | 0.0011% | 90,648 |
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
- CNTN3
- Protein
- p.Ser243=
- Coding
- c.729G>A
- MANE Select
- NM_020872
- dbSNP
- rs776282929
- Type
- single nucleotide variant
- Location
- chr3:74369921 (GRCh38)
- Gene constraint
- LOEUF 0.668 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.80 · 1 PDB
- Residue 243
- the ig-like c2-type 3 domain
Similar variants
- CNTN3 p.Ser243Leu Benign/Likely benign ★★ ⚠ same residue
- CNTN3 c.1669-4A>G Uncertain significance ★★ same type
- CNTN3 p.Arg841Gln Uncertain significance ★★ ⚠ same type
- CNTN3 p.Glu168Lys Uncertain significance ★★ ⚠ same type
- CNTN3 c.359-5A>C Benign ★★ same type
- CNTN3 c.56-10A>T Benign ★★ same type
- CNTN3 c.947-7A>G Benign ★★ same type
- CNTN3 p.Gln947= Benign ★★ 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/cntn3-p-ser243 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown