Is CNTNAP1 p.Tyr23= (c.69C>T) pathogenic?

CNTNAP1 p.Tyr23= (c.69C>T) is classified Likely benign in CNTNAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-07-16). Absent from gnomAD v4.1.

How common is CNTNAP1 p.Tyr23= (c.69C>T) in the general population?

CNTNAP1 p.Tyr23= (c.69C>T) is absent from gnomAD v4.1 (gnomAD).

CNTNAP1 p.Tyr23=

c.69C>T · VCV4808079

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,610,826)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>A here scores Δ0.89 · evaluated, not missing
Constraint at this position
Conservation	phyloP -4.3	GERP -4
Overall
CADD	6.589	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,610,826). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CNTNAP1
Protein: p.Tyr23=
Coding: c.69C>T
MANE Select: NM_003632
Type: single nucleotide variant
Location: chr17:42683822 (GRCh38)
Gene constraint: LOEUF 0.578 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.51

Full CNTNAP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CNTNAP1 p.Tyr23Ter Pathogenic ★ same residue
CNTNAP1 p.Tyr23His 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

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-tyr23 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown