# NM_000548.5(TSC2):c.90T>C (p.Ser30=)

https://sugi.bio/variant/tsc2-p-ser30

## Summary

**TSC2 p.Ser30= (c.90T>C)** is classified **Likely benign** in TSC2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-12-20). Absent from gnomAD v4.1; Associated with tuberous sclerosis 2.

**At a glance:** Likely benign · review: Multiple submitters · 2 submitters · 2 linked conditions · absent from gnomAD v4.1

## For patients & families {#patients}

This is a change in the TSC2 gene that is classified as likely benign — not considered disease-causing, submitted by 2 submitters, and is linked to tuberous sclerosis 2.

*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 dominant |
| Age of onset (of this condition) | All ages |
| Prevalence | 1-9 / 100 000 (Taiwan, Province of China) |
| Clinical trials | 4 registered for this condition — see ClinicalTrials.gov |
| Diagnostic panels | TSC2 is a diagnostic-grade gene on 21 Genomics England panels |

**Commonly reported features of Tuberous sclerosis complex** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Abnormality of the kidney — Very frequent (99-80%)
- Atypical behavior — Very frequent (99-80%)
- Seizure — Very frequent (99-80%)
- Cortical dysplasia — Very frequent (99-80%)
- Subependymal nodules — Very frequent (99-80%)
- Cortical tubers — Very frequent (99-80%)
- Hypomelanotic macule — Very frequent (99-80%)
- Generalized abnormality of skin — Very frequent (99-80%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0015640/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [TSC2](https://sugi.bio/atlas/gene/TSC2/) |
| Protein change (HGVS p.) | p.Ser30= |
| Coding change (HGVS c.) | c.90T>C |
| MANE Select transcript | [NM_000548](https://www.ncbi.nlm.nih.gov/nuccore/NM_000548) |
| Variant type | single nucleotide variant |
| Location | chr16:2048705-2048705 (GRCh38) |
| ClinVar | [VCV3628285](https://www.ncbi.nlm.nih.gov/clinvar/variation/3628285/) |

**All HGVS expressions:** `LRG_1366:g.4162A>G`, `LRG_487:g.4400T>C`, `LRG_487t1:c.90T>C`, `NC_000016.10:g.2048705T>C`, `NC_000016.9:g.2098706T>C`, `NG_005895.1:g.4400T>C`, `NG_008412.1:g.4162A>G`, `NM_000548.5:c.90T>C`, `NM_001077183.3:c.90T>C`, `NM_001114382.3:c.90T>C`, `NM_001318827.2:c.90T>C`, `NM_001318829.2:c.-10+640T>C`, `NM_001318831.2:c.-137T>C`, `NM_001318832.2:c.123T>C`, `NM_001363528.2:c.90T>C`, `NM_001370404.1:c.90T>C`, `NM_001370405.1:c.90T>C`, `NM_001406663.1:c.90T>C`, `NM_001406664.1:c.90T>C`, `NM_001406665.1:c.90T>C`, `NM_001406667.1:c.90T>C`, `NM_001406668.1:c.90T>C`, `NM_001406670.1:c.90T>C`, `NM_001406671.1:c.90T>C`, `NM_001406673.1:c.90T>C`, `NM_001406675.1:c.-10+640T>C`, `NM_001406676.1:c.-10+640T>C`, `NM_001406677.1:c.-10+640T>C`, `NM_001406678.1:c.90T>C`, `NM_001406679.1:c.-10+640T>C`, `NM_001406680.1:c.-727T>C`, `NM_001406681.1:c.-356T>C`, `NM_001406682.1:c.-137T>C`, `NM_001406683.1:c.-727T>C`, `NM_001406684.1:c.-137T>C`, `NM_001406685.1:c.-137T>C`, `NM_001406686.1:c.-89+640T>C`, `NM_001406687.1:c.-727T>C`, `NM_001406688.1:c.-137T>C`, `NM_001406689.1:c.-1342T>C`, `NM_001406690.1:c.-1342T>C`, `NM_001406691.1:c.-1342T>C`, `NM_001406692.1:c.-1342T>C`, `NM_001406693.1:c.-1648T>C`, `NM_001406694.1:c.-1223T>C`, `NM_001406695.1:c.-1223T>C`, `NM_001406696.1:c.-1330T>C`, `NM_001406697.1:c.-1342T>C`, `NM_001406698.1:c.-1518T>C`, `NM_021055.3:c.90T>C`, `NR_176225.1:n.200T>C`, `NR_176226.1:n.200T>C`, `NR_176227.1:n.200T>C`, `NR_176228.1:n.200T>C`, `NR_176229.1:n.200T>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 -0.274, GERP -2.24, phastCons 0.554 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- CADD: **PHRED 9.491**. 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: **below the reporting threshold**. This position is scored for a different substitution (T>A, Δ0.31 donor gain), so this allele was evaluated and its deltas all fell under Δ0.2 — a prediction of no splicing effect for this allele, not a gap in our data. *No ACMG code assigned.*
- Population frequency: **absent from gnomAD v4.1** — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

*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}

**TSC2** population constraint: LOEUF 0.203, pLI 1, missense-Z 0.17171; ClinGen dosage — haploinsufficiency 3, triplosensitivity 0 (0–3 scale). *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

## Protein context {#protein}

Residue **30** lies in the 'required for interaction with tsc1' region.

AlphaFold model confidence (whole protein): pLDDT 68.81, 13% of residues very-high.

**2 experimental structure(s)** (PDB): [7DL2](https://www.rcsb.org/structure/7DL2), [9CE3](https://www.rcsb.org/structure/9CE3).

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

*Describes the biological roles of TSC2 (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:** TSC2's established molecular role includes GTPase activator activity. p.Ser30= falls in the required for interaction with tsc1 region. In Reactome, TSC2 is annotated in disease pathway(s) including **Constitutive Signaling by AKT1 E17K in Cancer**.

**Disease mechanism (Reactome):** TSC2 loss or alteration is curated in [Constitutive Signaling by AKT1 E17K in Cancer](https://reactome.org/content/detail/R-HSA-5674400).

### Pathways affected {#pathways}

TSC2 participates in **7 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Constitutive Signaling by AKT1 E17K in Cancer](https://reactome.org/content/detail/R-HSA-5674400) | curated |
| [AKT phosphorylates targets in the cytosol](https://reactome.org/content/detail/R-HSA-198323) | curated |
| [Energy dependent regulation of mTOR by LKB1-AMPK](https://reactome.org/content/detail/R-HSA-380972) | curated |
| [Inhibition of TSC complex formation by AKT (PKB)](https://reactome.org/content/detail/R-HSA-165181) | curated |
| [Macroautophagy](https://reactome.org/content/detail/R-HSA-1632852) | curated |
| [TBC/RABGAPs](https://reactome.org/content/detail/R-HSA-8854214) | curated |
| [TP53 Regulates Metabolic Genes](https://reactome.org/content/detail/R-HSA-5628897) | curated |

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

**Molecular function:** GTPase activator activity, phosphatase binding, small GTPase binding, protein homodimerization activity, Hsp90 protein binding.

**Biological process:** cellular response to starvation, positive regulation of macroautophagy, negative regulation of TOR signaling, anoikis, negative regulation of TORC1 signaling.

## Clinical significance {#significance}

**Likely benign** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2024-12-20.

**Submitter consensus:** unanimous (2/2 Likely benign).

**Submission history:** 2 submissions (2024); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Ambry Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2024-12-20 |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2024-06-10 |

## Associated conditions {#conditions}

[tuberous sclerosis 2](https://sugi.bio/atlas/disease/tuberous-sclerosis-2/), [hereditary neoplastic syndrome](https://sugi.bio/atlas/disease/hereditary-neoplastic-syndrome/).

**Reported phenotype names (ClinVar):** Tuberous sclerosis 2, Hereditary cancer-predisposing syndrome, Neoplastic Syndromes, Hereditary, Tumor predisposition, Hereditary Cancer Syndrome, Hereditary neoplastic syndrome.

## Same-residue context {#hotspot}

Residue **30** carries **1 other pathogenic ClinVar variant** — a recurrently-mutated position: [TSC2 p.Ser30fs](/variant/tsc2-p-ser30fs). *Positional co-occurrence of independent ClinVar records, not functional proof.*

## Similar variants {#similar}

Related TSC2 variant pages (same residue, condition, or type): [TSC2 p.Ser30Cys](/variant/tsc2-p-ser30cys), [TSC2 c.1257+1G>A](/variant/tsc2-c-1257-plus-1g-a), [TSC2 c.1258-2A>G](/variant/tsc2-c-1258-minus-2a-g), [TSC2 c.1361+1G>A](/variant/tsc2-c-1361-plus-1g-a), [TSC2 c.1361+1G>T](/variant/tsc2-c-1361-plus-1g-t), [TSC2 c.1362-1G>A](/variant/tsc2-c-1362-minus-1g-a), [TSC2 c.138+2T>C](/variant/tsc2-c-138-plus-2t-c), [TSC2 c.138+5G>A](/variant/tsc2-c-138-plus-5g-a).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-06); 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 2026-07-14); 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 3628285). 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.*