# NM_000368.5(TSC1):c.1839A>T (p.Pro613=)

https://sugi.bio/variant/tsc1-p-pro613

## Summary

**TSC1 p.Pro613= (c.1839A>T)** is classified **Uncertain significance** in TSC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-22). Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

**At a glance:** Uncertain significance · review: Single submitter · 1 submitter · 1 linked condition · absent from gnomAD v4.1

## For patients & families {#patients}

This is a change in the TSC1 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 1 submitter, and is linked to hereditary neoplastic 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.*

|  |  |
| --- | --- |
| Clinical trials | 31 registered for this condition — see ClinicalTrials.gov |

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0019921/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [TSC1](https://sugi.bio/atlas/gene/TSC1/) |
| Protein change (HGVS p.) | p.Pro613= |
| Coding change (HGVS c.) | c.1839A>T |
| MANE Select transcript | [NM_000368](https://www.ncbi.nlm.nih.gov/nuccore/NM_000368) |
| Variant type | single nucleotide variant |
| Location | chr9:132905739-132905739 (GRCh38) |
| ClinVar | [VCV3974564](https://www.ncbi.nlm.nih.gov/clinvar/variation/3974564/) |

**All HGVS expressions:** `LRG_486:g.43895A>T`, `LRG_486t1:c.1839A>T`, `NC_000009.11:g.135781126T>A`, `NC_000009.12:g.132905739T>A`, `NG_012386.1:g.43895A>T`, `NM_000368.5:c.1839A>T`, `NM_001162426.2:c.1836A>T`, `NM_001162427.2:c.1686A>T`, `NM_001362177.2:c.1476A>T`, `NM_001406592.1:c.1839A>T`, `NM_001406593.1:c.1839A>T`, `NM_001406594.1:c.1839A>T`, `NM_001406595.1:c.1839A>T`, `NM_001406596.1:c.1839A>T`, `NM_001406597.1:c.1836A>T`, `NM_001406598.1:c.1836A>T`, `NM_001406599.1:c.1836A>T`, `NM_001406600.1:c.1836A>T`, `NM_001406601.1:c.1839A>T`, `NM_001406602.1:c.1839A>T`, `NM_001406603.1:c.1836A>T`, `NM_001406604.1:c.1836A>T`, `NM_001406605.1:c.1839A>T`, `NM_001406606.1:c.1839A>T`, `NM_001406607.1:c.1839A>T`, `NM_001406608.1:c.1836A>T`, `NM_001406609.1:c.1836A>T`, `NM_001406610.1:c.1686A>T`, `NM_001406611.1:c.1683A>T`, `NM_001406612.1:c.1683A>T`, `NM_001406613.1:c.1683A>T`, `NM_001406614.1:c.1476A>T`, `NM_001406615.1:c.1476A>T`, `NM_001406616.1:c.1476A>T`, `NM_001406617.1:c.1476A>T`, `NM_001406618.1:c.1476A>T`, `NM_001406619.1:c.1476A>T`, `NM_001406620.1:c.1473A>T`, `NM_001406621.1:c.1473A>T`, `NM_001406622.1:c.1473A>T`, `NM_001406623.1:c.1473A>T`, `NM_001406624.1:c.1476A>T`, `NM_001406625.1:c.1473A>T`, `NM_001406626.1:c.888A>T`, `NM_001406627.1:c.885A>T`, `NM_001406628.1:c.885A>T`, `NM_001406629.1:c.786A>T`, `NM_001406630.1:c.786A>T`, `NR_176214.1:n.2056A>T`, `NR_176215.1:n.2056A>T`, `NR_176216.1:n.1923A>T`, `NR_176217.1:n.2053A>T`, `NR_176218.1:n.2056A>T`

## 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 and, for splice-region changes, SpliceAI (below), not from a missing predictor score.
- SpliceAI predicts **acceptor gain** (Δ 0.37) — a splice-altering prediction on an uncertain variant — a signal for review
- Conservation: phyloP 4.314, GERP 1.05, phastCons 1 — highly conserved position (PP3-type support)
- CADD: **PHRED 18.24**. 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 deltas (raw): acceptor loss **0.00**, donor loss **0.00**, acceptor gain **0.37**, donor gain **0.00**. Largest is acceptor gain.
- SpliceAI deltas (masked): acceptor loss **0.00**, donor loss **0.00**, acceptor gain **0.37**, donor gain **0.00**.
- Pangolin: Δ**0.27** (gain), gain 0.27 / loss 0.00. Agrees with SpliceAI. An independent predictor to SpliceAI — a different model trained on different data. *Descriptive; ClinGen's SVI calibration covers SpliceAI, not Pangolin, so no ACMG code is 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}

**TSC1** population constraint: LOEUF 0.227, pLI 1, missense-Z 3.7116; ClinGen dosage — haploinsufficiency 3/3, triplosensitivity 0/3. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

## Protein context {#protein}

Residue **613** lies in the 'mediates interaction with wdr45b' region; an α-helix; a UniProt-annotated variant site (in tsc1).

AlphaFold model confidence (whole protein): pLDDT 63.55, 26% of residues very-high.

**5 experimental structure(s)** (PDB): [4Z6Y](https://www.rcsb.org/structure/4Z6Y), [5EJC](https://www.rcsb.org/structure/5EJC), [7DL2](https://www.rcsb.org/structure/7DL2), [9C9I](https://www.rcsb.org/structure/9C9I), [9CE3](https://www.rcsb.org/structure/9CE3).

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

*Describes the biological roles of TSC1 (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:** TSC1's established molecular role includes Hsp70 protein binding. p.Pro613= falls in the mediates interaction with wdr45b region.


### Pathways affected {#pathways}

TSC1 participates in **5 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [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:** Hsp70 protein binding, ATPase inhibitor activity, protein folding chaperone, protein-folding chaperone binding, Hsp90 protein binding.

**Biological process:** regulation of cell-matrix adhesion, cell-matrix adhesion, negative regulation of cell population proliferation, cellular response to starvation, negative regulation of TOR signaling, negative regulation of ATP-dependent activity.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2025-05-22.

**Submitter consensus:** unanimous (1/1 Uncertain significance).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Ambry Genetics | Uncertain significance | criteria provided, single submitter | clinical testing | 2025-05-22 |

## Associated conditions {#conditions}

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

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

## Similar variants {#similar}

Related TSC1 variant pages (same residue, condition, or type): [TSC1 p.Pro613Ser](/variant/tsc1-p-pro613ser), [TSC1 c.1029+1G>A](/variant/tsc1-c-1029-plus-1g-a), [TSC1 c.1997+2T>G](/variant/tsc1-c-1997-plus-2t-g), [TSC1 c.1998-1G>T](/variant/tsc1-c-1998-minus-1g-t), [TSC1 c.2042-5A>G](/variant/tsc1-c-2042-minus-5a-g), [TSC1 c.2208+2T>A](/variant/tsc1-c-2208-plus-2t-a), [TSC1 c.2626-2A>C](/variant/tsc1-c-2626-minus-2a-c), [TSC1 c.664-15A>G](/variant/tsc1-c-664-minus-15a-g).

### 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 2026-10-14); 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 3974564). 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.*