# NM_004064.5(CDKN1B):c.33T>C (p.Pro11=)

https://sugi.bio/variant/cdkn1b-p-pro11

## Summary

**CDKN1B p.Pro11= (c.33T>C)** is classified **Likely benign** in CDKN1B (ClinVar, Single submitter, 1 submitter; last evaluated 2019-09-05). Very rare (popmax 0.000339%, nfe); Associated with hereditary neoplastic syndrome.

**At a glance:** Likely benign · review: Single submitter · rsID rs2136355399 · 1 submitter · 1 linked condition · very rare (popmax 0.000339%, nfe)

## For patients & families {#patients}

This is a change in the CDKN1B gene that is classified as likely benign — not considered disease-causing, 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 | [CDKN1B](https://sugi.bio/atlas/gene/CDKN1B/) |
| Protein change (HGVS p.) | p.Pro11= |
| Coding change (HGVS c.) | c.33T>C |
| MANE Select transcript | [NM_004064](https://www.ncbi.nlm.nih.gov/nuccore/NM_004064) |
| dbSNP | [rs2136355399](https://www.ncbi.nlm.nih.gov/snp/rs2136355399/) |
| Variant type | single nucleotide variant |
| Location | chr12:12717872-12717872 (GRCh38) |
| ClinVar | [VCV1731057](https://www.ncbi.nlm.nih.gov/clinvar/variation/1731057/) |

**All HGVS expressions:** `NC_000012.11:g.12870806T>C`, `NC_000012.12:g.12717872T>C`, `NG_016341.1:g.5505T>C`, `NM_004064.5:c.33T>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 0.95, GERP -2.83, phastCons 1 — weakly conserved position
- CADD: **PHRED 10.71**. 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 **0.000339%** (nfe) · FAF95 7.9e-05% · FAF99 5.4e-05% · 4/1,179,988 in the highest group · 4/1,613,728 alleles overall — very rare (popmax 0.000339%, nfe).

*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}

**CDKN1B** population constraint: LOEUF 0.804, pLI 0.24233, missense-Z -1.3002; 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.*

Curated gene–disease validity (ClinGen):

- **multiple endocrine neoplasia type 4** — Definitive (AD)
- **hereditary nonpolyposis colon cancer** — Limited (AR)

## Protein context {#protein}

Residue **11** lies in the 'disordered' region.

AlphaFold model confidence (whole protein): pLDDT 71.08, 36% of residues very-high.

**19 experimental structure(s)** (PDB): [1H27](https://www.rcsb.org/structure/1H27), [1JSU](https://www.rcsb.org/structure/1JSU), [2AST](https://www.rcsb.org/structure/2AST), [5UQ3](https://www.rcsb.org/structure/5UQ3), [6ATH](https://www.rcsb.org/structure/6ATH), [6P8E](https://www.rcsb.org/structure/6P8E).

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

*Describes the biological roles of CDKN1B (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:** CDKN1B's established molecular role includes protein kinase inhibitor activity. p.Pro11= falls in the disordered region. In Reactome, CDKN1B is annotated in disease pathway(s) including **Constitutive Signaling by AKT1 E17K in Cancer**, **Defective binding of RB1 mutants to E2F1,(E2F2, E2F3)**.

**Disease mechanism (Reactome):** CDKN1B loss or alteration is curated in [Constitutive Signaling by AKT1 E17K in Cancer](https://reactome.org/content/detail/R-HSA-5674400), [Defective binding of RB1 mutants to E2F1,(E2F2, E2F3)](https://reactome.org/content/detail/R-HSA-9661069).

### Pathways affected {#pathways}

CDKN1B participates in **16 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Constitutive Signaling by AKT1 E17K in Cancer](https://reactome.org/content/detail/R-HSA-5674400) | curated |
| ⚕ [Defective binding of RB1 mutants to E2F1,(E2F2, E2F3)](https://reactome.org/content/detail/R-HSA-9661069) | curated |
| [AKT phosphorylates targets in the cytosol](https://reactome.org/content/detail/R-HSA-198323) | curated |
| [Cyclin A:Cdk2-associated events at S phase entry](https://reactome.org/content/detail/R-HSA-69656) | curated |
| [Cyclin D associated events in G1](https://reactome.org/content/detail/R-HSA-69231) | curated |
| [Cyclin E associated events during G1/S transition ](https://reactome.org/content/detail/R-HSA-69202) | curated |
| [DNA Damage/Telomere Stress Induced Senescence](https://reactome.org/content/detail/R-HSA-2559586) | curated |
| [Estrogen-dependent nuclear events downstream of ESR-membrane signaling](https://reactome.org/content/detail/R-HSA-9634638) | curated |
| [FLT3 Signaling](https://reactome.org/content/detail/R-HSA-9607240) | curated |
| [PTK6 Regulates Cell Cycle](https://reactome.org/content/detail/R-HSA-8849470) | curated |
| [SCF(Skp2)-mediated degradation of p27/p21](https://reactome.org/content/detail/R-HSA-187577) | curated |
| [Senescence-Associated Secretory Phenotype (SASP)](https://reactome.org/content/detail/R-HSA-2559582) | curated |
| [TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest](https://reactome.org/content/detail/R-HSA-6804116) | curated |
| [p53-Dependent G1 DNA Damage Response](https://reactome.org/content/detail/R-HSA-69563) | curated |
| [FOXO-mediated transcription of cell cycle genes](https://reactome.org/content/detail/R-HSA-9617828) | electronic |
| [RHO GTPases activate CIT](https://reactome.org/content/detail/R-HSA-5625900) | electronic |

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

**Molecular function:** protein kinase inhibitor activity, cyclin-dependent protein serine/threonine kinase inhibitor activity, protein kinase binding, protein phosphatase binding, cyclin-dependent protein kinase regulator activity, cyclin binding.

**Biological process:** regulation of cyclin-dependent protein serine/threonine kinase activity, negative regulation of cell population proliferation, negative regulation of cell growth, positive regulation of protein catabolic process, autophagic cell death, nuclear export.

## Clinical significance {#significance}

**Likely benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2019-09-05.

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

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Ambry Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2019-09-05 |

## Associated conditions {#conditions}

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

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

## Similar variants {#similar}

Related CDKN1B variant pages (same residue, condition, or type): [CDKN1B p.Pro11Ala](/variant/cdkn1b-p-pro11ala), [CDKN1B p.Pro11Arg](/variant/cdkn1b-p-pro11arg), [CDKN1B p.Pro11Leu](/variant/cdkn1b-p-pro11leu), [CDKN1B p.Pro11Ser](/variant/cdkn1b-p-pro11ser), [CDKN1B p.Arg154Ter](/variant/cdkn1b-p-arg154ter), [CDKN1B p.Arg5Ter](/variant/cdkn1b-p-arg5ter), [CDKN1B p.Gln104Ter](/variant/cdkn1b-p-gln104ter), [CDKN1B p.Gln107Ter](/variant/cdkn1b-p-gln107ter).

### 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 1731057). 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.*