# NM_014141.6(CNTNAP2):c.2976T>C (p.Ser992=)

https://sugi.bio/variant/cntnap2-p-ser992

## Summary

**CNTNAP2 p.Ser992= (c.2976T>C)** is classified **Likely benign** in CNTNAP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-07-27). Very rare (popmax 0.00133%, afr); Associated with cortical dysplasia-focal epilepsy syndrome.

**At a glance:** Likely benign · review: Single submitter · rsID rs1240944880 · 1 submitter · 1 linked condition · very rare (popmax 0.00133%, afr)

## For patients & families {#patients}

This is a change in the CNTNAP2 gene that is classified as likely benign — not considered disease-causing, submitted by 1 submitter, and is linked to cortical dysplasia-focal epilepsy syndrome.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

|  |  |
| --- | --- |
| Typical inheritance (of this condition) | Autosomal recessive |
| Age of onset (of this condition) | Infancy |
| Diagnostic panels | CNTNAP2 is a diagnostic-grade gene on 8 Genomics England panels |

**Commonly reported features of CNTNAP2-related developmental and epileptic encephalopathy** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Delayed speech and language development — Very frequent (99-80%)
- Seizure — Very frequent (99-80%)
- Abnormality of neuronal migration — Very frequent (99-80%)
- Focal-onset seizure — Very frequent (99-80%)
- Abnormal neuron morphology — Very frequent (99-80%)
- Delayed ability to walk — Very frequent (99-80%)
- Global developmental delay — Frequent (79-30%)
- Mental deterioration — Frequent (79-30%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0016997/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [CNTNAP2](https://sugi.bio/atlas/gene/CNTNAP2/) |
| Protein change (HGVS p.) | p.Ser992= |
| Coding change (HGVS c.) | c.2976T>C |
| MANE Select transcript | [NM_014141](https://www.ncbi.nlm.nih.gov/nuccore/NM_014141) |
| dbSNP | [rs1240944880](https://www.ncbi.nlm.nih.gov/snp/rs1240944880/) |
| Variant type | single nucleotide variant |
| Location | chr7:148172444-148172444 (GRCh38) |
| ClinVar | [VCV1088670](https://www.ncbi.nlm.nih.gov/clinvar/variation/1088670/) |

**All HGVS expressions:** `NC_000007.13:g.147869536T>C`, `NC_000007.14:g.148172444T>C`, `NG_007092.3:g.2061444T>C`, `NM_014141.6:c.2976T>C`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation (below), not from a missing predictor score.
- Conservation: phyloP -3.607 — fast-evolving / accelerated position
- CADD: **PHRED 0.4**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- SpliceAI: **not assessed** — no allele at this position is in our SpliceAI release, either because it lies outside the scored MANE transcript scope or because every allele is below Δ0.2. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): grpmax **0.00133%** (afr) · 1/74,936 in the highest group · 1/1,614,102 alleles overall — very rare (popmax 0.00133%, afr).

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**CNTNAP2** population constraint: LOEUF 0.721, pLI 1.9949e-18, missense-Z 0.26666; ClinGen dosage — haploinsufficiency 1/3, triplosensitivity 0/3. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

Curated gene–disease validity (ClinGen):

- **complex neurodevelopmental disorder** — Definitive (AR)
- **complex neurodevelopmental disorder** — Disputed (AD)

## Protein context {#protein}

Residue **992** lies in the egf-like 2 domain.

AlphaFold model confidence (whole protein): pLDDT 83.81, 58% of residues very-high.

**1 experimental structure(s)** (PDB): [5Y4M](https://www.rcsb.org/structure/5Y4M).

## What this gene does {#gene-function}

*Describes the biological roles of CNTNAP2 (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*

**How this variant is thought to act:** CNTNAP2's established molecular role includes enzyme binding. p.Ser992= falls in the egf-like 2 domain.


### Molecular function & processes (GO — experimentally supported) {#go}

**Molecular function:** enzyme binding.

**Biological process:** learning, cell population proliferation, striatum development, limbic system development, thalamus development, cerebral cortex development.

## Clinical significance {#significance}

**Likely benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2020-07-27.

**Submitter consensus:** unanimous (1/1 Likely benign).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2020-07-27 |

## Associated conditions {#conditions}

[cortical dysplasia-focal epilepsy syndrome](https://sugi.bio/atlas/disease/cortical-dysplasia-focal-epilepsy-syndrome/).

**Reported phenotype names (ClinVar):** Cortical dysplasia-focal epilepsy syndrome, Pitt-Hopkins-like syndrome 1.

## Similar variants {#similar}

Related CNTNAP2 variant pages (same residue, condition, or type): [CNTNAP2 c.1348+1G>A](/variant/cntnap2-c-1348-plus-1g-a), [CNTNAP2 c.3382-2A>C](/variant/cntnap2-c-3382-minus-2a-c), [CNTNAP2 c.97+1G>A](/variant/cntnap2-c-97-plus-1g-a), [CNTNAP2 p.Arg1088Ter](/variant/cntnap2-p-arg1088ter), [CNTNAP2 p.Arg1095Ter](/variant/cntnap2-p-arg1095ter), [CNTNAP2 p.Arg483Ter](/variant/cntnap2-p-arg483ter), [CNTNAP2 p.Gln1111Ter](/variant/cntnap2-p-gln1111ter), [CNTNAP2 p.Gln297Ter](/variant/cntnap2-p-gln297ter).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-14); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-10-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 1088670). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*