CNTNAP1 p.Pro993=
c.2979A>G · rs61738809 · VCV712209
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.59%, 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 -5.1 | GERP -5.5 |
| Overall | ||
| CADD | 0.42 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.59%
African / African-American · 1,193/75,024 alleles
Filtering AF
1.52%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.48%
Overall
0.0826%
1,333/1,613,348 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.59% | 63 |
| Remaining individualsnot grpmax-eligible | 0.0912% | 1,096 |
| Admixed American | 0.0583% | 1,715 |
| Middle Eastern | 0.0495% | 2,020 |
| South Asian | 0.00769% | 13,012 |
| European (non-Finnish) | 0.00322% | 31,034 |
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
- CNTNAP1
- Protein
- p.Pro993=
- Coding
- c.2979A>G
- MANE Select
- NM_003632
- dbSNP
- rs61738809
- Type
- single nucleotide variant
- Location
- chr17:42693523 (GRCh38)
- Gene constraint
- LOEUF 0.578 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.51
- Residue 993
- the egf-like 2 domain; a disulfide bond; a UniProt-annotated variant site (in chn3); a UniProt-annotated variant site (in lccs7 and chn3); a UniProt-annotated variant site (in lccs7)
Similar variants
- CNTNAP1 p.Pro993Leu Uncertain significance ★★ ⚠ same residue
- CNTNAP1 p.Arg1121Ter Pathogenic ★★ same type
- CNTNAP1 p.Arg618Ter Pathogenic/Likely pathogenic ★★ same type
- CNTNAP1 p.Arg697Ter Pathogenic/Likely pathogenic ★★ same type
- CNTNAP1 p.Arg835Ter Pathogenic ★★ same type
- CNTNAP1 p.Arg890Ter Pathogenic ★★ same type
- CNTNAP1 p.Trp672Ter Pathogenic ★★ same type
- CNTNAP1 c.3568+10G>A Uncertain significance ★★ 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/cntnap1-p-pro993 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown