CNTNAP2 p.Ser451=
c.1353T>C · rs1794916255 · VCV1131010
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
Conditions
2
Inborn genetic diseases
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 -0.61 | GERP -0.89, phastCons 0.059 |
| Overall | ||
| CADD | 7.816 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/74,924 alleles
Overall
6.2e-05%
1/1,613,936 alleles · very rare
exomes 0/1,461,700 · genomes 1/152,236 · joint denominator
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
- CNTNAP2
- Protein
- p.Ser451=
- Coding
- c.1353T>C
- MANE Select
- NM_014141
- dbSNP
- rs1794916255
- Type
- single nucleotide variant
- Location
- chr7:147300145 (GRCh38)
- Gene constraint
- LOEUF 0.721 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 83.81 · 1 PDB
- Residue 451
- the laminin g-like 2 domain
Similar variants
- CNTNAP2 c.1348+1G>A Likely pathogenic ★★ same condition
- CNTNAP2 c.3382-2A>C Likely pathogenic ★★ same condition
- CNTNAP2 c.97+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CNTNAP2 p.Arg1088Ter Pathogenic/Likely pathogenic ★★ same condition
- CNTNAP2 p.Arg1095Ter Pathogenic/Likely pathogenic ★★ same condition
- CNTNAP2 p.Arg483Ter Pathogenic/Likely pathogenic ★★ same condition
- CNTNAP2 p.Gln1111Ter Pathogenic/Likely pathogenic ★★ same condition
- CNTNAP2 p.Gln297Ter 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/cntnap2-p-ser451 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown