Is CNTNAP1 p.Ser343fs (c.1027_1029delinsCA) pathogenic?

CNTNAP1 p.Ser343fs (c.10271029delinsCA) is classified Likely pathogenic in CNTNAP1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-07-15). Associated with CNTNAP1-related disorder.

What condition is associated with CNTNAP1 p.Ser343fs (c.1027_1029delinsCA)?

CNTNAP1 p.Ser343fs (c.1027_1029delinsCA) is associated with CNTNAP1-related disorder (ClinVar).

CNTNAP1 p.Ser343fs

c.1027_1029delinsCA · VCV3347070

Likely pathogenic No assertion criteria

Classification

Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

CNTNAP1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 7 of 24
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.5	GERP 2.2, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Variant & gene context

Gene: CNTNAP1
Protein: p.Ser343fs
Coding: c.1027_1029delinsCA
MANE Select: NM_003632
Type: Indel
Location: chr17:42687029 (GRCh38)
Gene constraint: LOEUF 0.578 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.51
Residue 343: a disulfide bond; the laminin g-like 1 domain

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

Disease context

CNTNAP1-related disorder

Similar variants

CNTNAP1 p.Ser343Phe Uncertain significance ★★ ⚠ same residue
CNTNAP1 c.2060-1G>A Likely pathogenic ★ same condition
CNTNAP1 p.Arg270Ter Pathogenic ★ same condition
CNTNAP1 p.Gln1132Ter Likely pathogenic ★ same condition
CNTNAP1 p.Gln671Ter Pathogenic ★ same condition
CNTNAP1 c.1_1629-1del Likely pathogenic same condition
CNTNAP1 p.Val928fs Likely pathogenic same condition
CNTNAP1 p.Arg1150Ser 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/cntnap1-p-ser343fs (accessed [today's date]).

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