Provide a comprehensive cross-database identifier and functional mapping reference for human CCND1. This should serve as a definitive lookup resource for researchers. ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ SECTION 1: GENE IDENTIFIERS ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Provide ALL gene-level database identifiers: - HGNC ID and approved symbol - Ensembl gene ID (ENSG) - NCBI Entrez Gene ID - OMIM gene/locus ID - Genomic location: chromosome, start position, end position, strand ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ SECTION 2: TRANSCRIPT IDENTIFIERS ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ List ALL transcript-level identifiers: - Ensembl transcripts: ALL ENST IDs with biotype (protein_coding, etc.) How many total transcripts? - RefSeq transcripts: ALL NM_ mRNA accessions Mark which is MANE Select (canonical clinical standard) - CCDS IDs: ALL consensus coding sequence identifiers For the CANONICAL/MANE SELECT transcript: - List ALL exon IDs (ENSE) with genomic coordinates - Total exon count ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ SECTION 3: PROTEIN IDENTIFIERS ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ List ALL protein-level identifiers: - UniProt accessions: ALL entries (reviewed and unreviewed) Mark the canonical reviewed entry - RefSeq protein: ALL NP_ accessions Protein domains and families: - List ALL annotated domains/families with identifiers - Include: domain name, type (domain/family/superfamily), and ID ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ SECTION 4: STRUCTURE IDENTIFIERS ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Experimental structures: - List ALL PDB structure IDs - For each: experimental method (X-ray, NMR, Cryo-EM) and resolution - Total PDB structure count Predicted structures: - AlphaFold model ID and confidence metrics (pLDDT) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ SECTION 5: CROSS-SPECIES ORTHOLOGS ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ List orthologous genes in key model organisms (where available): - Mouse (Mus musculus): gene ID, symbol - Rat (Rattus norvegicus): gene ID, symbol - Zebrafish (Danio rerio): gene ID, symbol - Fruit fly (Drosophila melanogaster): gene ID, symbol - Worm (C. elegans): gene ID, symbol - Yeast (S. cerevisiae): gene ID, symbol ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ SECTION 6: CLINICAL VARIANTS & AI PREDICTIONS ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Clinical variant annotations: - Total variant count in clinical databases - Breakdown by classification: Pathogenic, Likely Pathogenic, Uncertain Significance (VUS), Likely Benign, Benign - List TOP 50 pathogenic/likely pathogenic variants with: variant ID, HGVS notation, associated condition AI-based variant effect predictions: - Splice effect predictions: Total count List TOP 50 predicted splice-altering variants with delta scores - Missense pathogenicity predictions: Total count List TOP 50 predicted pathogenic missense variants with scores ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ SECTION 7: BIOLOGICAL PATHWAYS & GENE ONTOLOGY ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Pathway membership: - List ALL biological pathways this gene participates in - Include pathway IDs and names - Total pathway count Gene Ontology annotations: - Biological Process: count and TOP 20 terms with IDs - Molecular Function: count and TOP 20 terms with IDs - Cellular Component: count and TOP 20 terms with IDs ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ SECTION 8: PROTEIN INTERACTIONS & MOLECULAR NETWORKS ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Protein-protein interactions: - Total interaction count - List TOP 50 highest-confidence interacting proteins with scores Protein similarity (evolutionary and structural): - Structural/embedding similarity: How many similar proteins? List TOP 20 with similarity scores - Sequence homology: How many homologous proteins? List TOP 20 with identity/similarity scores ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ SECTION 9: TRANSCRIPTION FACTOR REGULATORY DATA ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ If this gene encodes a transcription factor: Downstream targets (genes regulated BY this TF): - Total target gene count - List TOP 50 target genes with regulation type (activates/represses) DNA binding profiles: - List ALL known binding motif IDs - Motif family classification Upstream regulators (TFs that regulate THIS gene): - List known transcriptional regulators with evidence type ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ SECTION 10: DRUG & PHARMACOLOGY DATA ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ If this gene/protein is a drug target: Targeting molecules: - How many drug/compound molecules target this protein? - List TOP 30 molecules by development phase - Include: molecule ID, name, mechanism, highest development phase Clinical trials: - How many clinical trials involve drugs targeting this gene? - List TOP 20 trials with: trial ID, phase, status, intervention Pharmacogenomics: - Known drug-gene interactions affecting drug response - Dosing guidelines if any exist ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ SECTION 11: EXPRESSION PROFILES ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Tissue expression: - Which tissues express this gene most highly? - List TOP 30 tissues with expression scores/levels - Note any tissue-specific or tissue-enriched patterns Cell type expression: - Which cell types show highest expression? - List TOP 30 cell types with expression scores - Note any cell type-specific patterns Single-cell expression data (if available): - Which single-cell datasets/experiments include this gene? - Notable cell population patterns ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ SECTION 12: DISEASE ASSOCIATIONS ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Mendelian/monogenic disease links: - What diseases are caused by mutations in this gene? - List ALL associated diseases with: disease name, disease ID, inheritance pattern, evidence level Phenotype associations: - What clinical phenotypes are associated with this gene? - List TOP 50 phenotype terms with IDs Complex trait associations (GWAS): - What traits/diseases are linked via genome-wide association studies? - List TOP 30 GWAS associations with: trait, study ID, p-value, effect size if available ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ FORMATTING REQUIREMENTS ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ - Present each section with clear headers - Use tables for listing multiple items - Always include COUNTS for every category - For lists with 50 items: show total count + TOP 50 - For lists with

Question

Provide a comprehensive cross-database identifier and functional mapping
reference for human CCND1. This should serve as a definitive
lookup resource for researchers.

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
SECTION 1: GENE IDENTIFIERS
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Provide ALL gene-level database identifiers:
- HGNC ID and approved symbol
- Ensembl gene ID (ENSG)
- NCBI Entrez Gene ID
- OMIM gene/locus ID
- Genomic location: chromosome, start position, end position, strand

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
SECTION 2: TRANSCRIPT IDENTIFIERS
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
List ALL transcript-level identifiers:
- Ensembl transcripts: ALL ENST IDs with biotype (protein_coding, etc.)
  How many total transcripts?
- RefSeq transcripts: ALL NM_ mRNA accessions
  Mark which is MANE Select (canonical clinical standard)
- CCDS IDs: ALL consensus coding sequence identifiers

For the CANONICAL/MANE SELECT transcript:
- List ALL exon IDs (ENSE) with genomic coordinates
- Total exon count

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
SECTION 3: PROTEIN IDENTIFIERS
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
List ALL protein-level identifiers:
- UniProt accessions: ALL entries (reviewed and unreviewed)
  Mark the canonical reviewed entry
- RefSeq protein: ALL NP_ accessions

Protein domains and families:
- List ALL annotated domains/families with identifiers
- Include: domain name, type (domain/family/superfamily), and ID

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
SECTION 4: STRUCTURE IDENTIFIERS
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Experimental structures:
- List ALL PDB structure IDs
- For each: experimental method (X-ray, NMR, Cryo-EM) and resolution
- Total PDB structure count

Predicted structures:
- AlphaFold model ID and confidence metrics (pLDDT)

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
SECTION 5: CROSS-SPECIES ORTHOLOGS
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
List orthologous genes in key model organisms (where available):
- Mouse (Mus musculus): gene ID, symbol
- Rat (Rattus norvegicus): gene ID, symbol
- Zebrafish (Danio rerio): gene ID, symbol
- Fruit fly (Drosophila melanogaster): gene ID, symbol
- Worm (C. elegans): gene ID, symbol
- Yeast (S. cerevisiae): gene ID, symbol

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
SECTION 6: CLINICAL VARIANTS & AI PREDICTIONS
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Clinical variant annotations:
- Total variant count in clinical databases
- Breakdown by classification: Pathogenic, Likely Pathogenic,
  Uncertain Significance (VUS), Likely Benign, Benign
- List TOP 50 pathogenic/likely pathogenic variants with:
  variant ID, HGVS notation, associated condition

AI-based variant effect predictions:
- Splice effect predictions: Total count
  List TOP 50 predicted splice-altering variants with delta scores
- Missense pathogenicity predictions: Total count
  List TOP 50 predicted pathogenic missense variants with scores

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
SECTION 7: BIOLOGICAL PATHWAYS & GENE ONTOLOGY
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Pathway membership:
- List ALL biological pathways this gene participates in
- Include pathway IDs and names
- Total pathway count

Gene Ontology annotations:
- Biological Process: count and TOP 20 terms with IDs
- Molecular Function: count and TOP 20 terms with IDs
- Cellular Component: count and TOP 20 terms with IDs

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
SECTION 8: PROTEIN INTERACTIONS & MOLECULAR NETWORKS
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Protein-protein interactions:
- Total interaction count
- List TOP 50 highest-confidence interacting proteins with scores

Protein similarity (evolutionary and structural):
- Structural/embedding similarity: How many similar proteins?
  List TOP 20 with similarity scores
- Sequence homology: How many homologous proteins?
  List TOP 20 with identity/similarity scores

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
SECTION 9: TRANSCRIPTION FACTOR REGULATORY DATA
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
If this gene encodes a transcription factor:

Downstream targets (genes regulated BY this TF):
- Total target gene count
- List TOP 50 target genes with regulation type (activates/represses)

DNA binding profiles:
- List ALL known binding motif IDs
- Motif family classification

Upstream regulators (TFs that regulate THIS gene):
- List known transcriptional regulators with evidence type

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
SECTION 10: DRUG & PHARMACOLOGY DATA
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
If this gene/protein is a drug target:

Targeting molecules:
- How many drug/compound molecules target this protein?
- List TOP 30 molecules by development phase
- Include: molecule ID, name, mechanism, highest development phase

Clinical trials:
- How many clinical trials involve drugs targeting this gene?
- List TOP 20 trials with: trial ID, phase, status, intervention

Pharmacogenomics:
- Known drug-gene interactions affecting drug response
- Dosing guidelines if any exist

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
SECTION 11: EXPRESSION PROFILES
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Tissue expression:
- Which tissues express this gene most highly?
- List TOP 30 tissues with expression scores/levels
- Note any tissue-specific or tissue-enriched patterns

Cell type expression:
- Which cell types show highest expression?
- List TOP 30 cell types with expression scores
- Note any cell type-specific patterns

Single-cell expression data (if available):
- Which single-cell datasets/experiments include this gene?
- Notable cell population patterns

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
SECTION 12: DISEASE ASSOCIATIONS
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Mendelian/monogenic disease links:
- What diseases are caused by mutations in this gene?
- List ALL associated diseases with: disease name, disease ID,
  inheritance pattern, evidence level

Phenotype associations:
- What clinical phenotypes are associated with this gene?
- List TOP 50 phenotype terms with IDs

Complex trait associations (GWAS):
- What traits/diseases are linked via genome-wide association studies?
- List TOP 30 GWAS associations with: trait, study ID, p-value,
  effect size if available

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
FORMATTING REQUIREMENTS
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
- Present each section with clear headers
- Use tables for listing multiple items
- Always include COUNTS for every category
- For lists with >50 items: show total count + TOP 50
- For lists with <50 items: show ALL items
- Always include database identifiers (IDs), not just names
- Mark canonical/primary/reviewed entries where applicable
- If a section has no data available, state "No data available"
  rather than omitting the section

Accepted Answer

Now let me compile the comprehensive reference document for CCND1.
CCND1 (Cyclin D1) - Comprehensive Cross-Database Reference ██████╗ ██████╗███╗ ██╗██████╗ ██╗ ██╔════╝██╔════╝████╗ ██║██╔══██╗███║ ██║ ██║ ██╔██╗ ██║██║ ██║╚██║ ██║ ██║ ██║╚██╗██║██║ ██║ ██║ ╚██████╗╚██████╗██║ ╚████║██████╔╝ ██║ ╚═════╝ ╚═════╝╚═╝ ╚═══╝╚═════╝ ╚═╝
Section 1: Gene Identifiers
DatabaseIdentifierNotes HGNC IDHGNC:1582Approved HGNC SymbolCCND1Approved symbol Gene Namecyclin D1Full name Ensembl …

Attribute	Value
Chromosome	11
Cytogenetic Band	11q13.3
Start Position	69,641,143
End Position	69,654,474
Strand	+ (forward)
Gene Length	13,331 bp

Type	Values
Previous Symbols	BCL1, D11S287E, PRAD1
Aliases	U21B31
Previous Names	cyclin D1 (PRAD1: parathyroid adenomatosis 1)
Gene Group	Cyclins

Transcript ID	Biotype	Start	End	UTR5	UTR3
ENST00000227507	protein_coding	69,641,156	69,654,474	69,641,156-69,641,313	69,651,283-69,654,474
ENST00000913508	protein_coding	69,641,143	69,654,474	69,641,143-69,641,313	69,651,283-69,654,474
ENST00000536559	protein_coding	69,641,206	69,648,240	69,641,206-69,641,313	69,648,000-69,648,240
ENST00000535993	retained_intron	69,641,231	69,643,317	-	-
ENST00000539241	retained_intron	69,641,165	69,644,188	-	-
ENST00000542367	retained_intron	69,647,957	69,651,407	-	-
ENST00000545484	retained_intron	69,643,712	69,648,143	-	-

Exon ID	Start	End	Strand
ENSE00001330774	69,641,156	69,641,511	+
ENSE00003684720	69,643,031	69,643,246	+
ENSE00000737399	69,643,832	69,643,991	+
ENSE00000894874	69,647,994	69,648,142	+
ENSE00000894873	69,651,118	69,654,474	+

Accession	Name	Status	Length	Mass
P24385	G1/S-specific cyclin-D1	✓ Reviewed (Canonical)	295 aa	33,729 Da
F5H437	-	Unreviewed	-	-
Q6FI00	-	Unreviewed	-	-

CCND1 Gene Complete Identifier and Functional Mapping Reference

Structured Data Sources

Database	Identifier	Notes
HGNC ID	HGNC:1582	Approved
HGNC Symbol	CCND1	Approved symbol
Gene Name	cyclin D1	Full name
Ensembl Gene	ENSG00000110092	Human
NCBI Entrez	595	Gene ID
OMIM	168461	Gene/locus
Locus Group	protein-coding gene
Locus Type	gene with protein product

InterPro ID	Name	Type
IPR006671	Cyclin_N	Domain
IPR004367	Cyclin_C-dom	Domain
IPR013763	Cyclin-like_dom	Domain
IPR039361	Cyclin	Family
IPR036915	Cyclin-like_sf	Homologous_superfamily
IPR048258	Cyclins_cyclin-box	Conserved_site

PDB ID	Title	Method	Resolution
2W96	CDK4 in complex with D-type cyclin	X-RAY	2.30 Å
2W9Z	CDK4 in complex with D-type cyclin	X-RAY	2.45 Å
6P8E	CDK4 with CyclinD1 and P27	X-RAY	2.30 Å
9CSK	CDK4 cyclin D1 with atirmociclib	X-RAY	2.25 Å
5VZU	Skp1-FBXO31-cyclin D1 complex	X-RAY	2.70 Å
2W99	CDK4 in complex with D-type cyclin	X-RAY	2.80 Å
6P8G	CDK4 with CyclinD1 and P27	X-RAY	2.80 Å
2W9F	CDK4 in complex with D-type cyclin	X-RAY	2.85 Å
6P8F	CDK4 with CyclinD1 and P27	X-RAY	2.89 Å
6P8H	CDK4 with CyclinD1 and P21	X-RAY	3.19 Å
9IVD	CyclinD1 bound AMBRA1-DDB1	CRYO-EM	3.55 Å

Organism	Gene ID	Symbol	Biotype
Mouse (Mus musculus)	ENSMUSG00000070348	Ccnd1	protein_coding
Rat (Rattus norvegicus)	ENSRNOG00000020918	Ccnd1	protein_coding
Zebrafish (Danio rerio)	ENSDARG00000101637	ccnd1	protein_coding
Fruit fly (D. melanogaster)	FBGN0010315	CycD	protein_coding
Fruit fly (D. melanogaster)	FBGN0000404	CycA	protein_coding (paralog)
Fruit fly (D. melanogaster)	FBGN0000405	CycB	protein_coding (paralog)
Fruit fly (D. melanogaster)	FBGN0010382	CycE	protein_coding (paralog)
Worm (C. elegans)	WBGENE00000867	cyb-2.2	protein_coding
Worm (C. elegans)	WBGENE00000871	cye-1	protein_coding

Classification	Count
Benign	6
Benign/Likely benign	1
Likely benign	4
Uncertain significance (VUS)	17
Likely pathogenic	1
Not provided	21

Variant ID	HGVS Notation	Type
2297468	c.785C>T (p.Ala262Val)	SNV
2299476	c.691C>G (p.Arg231Gly)	SNV
2341922	c.868G>A (p.Val290Met)	SNV
2391496	c.800A>G (p.Asp267Gly)	SNV
2489951	c.569C>T (p.Ala190Val)	SNV
2554042	c.753C>G (p.Ile251Met)	SNV
2581321	c.387_392delinsGGAG (p.Asp129fs)	Indel
2610543	c.560C>T (p.Ala187Val)	SNV

Variant	Effect	Delta Score
11:69641464:G:GT	donor_gain	1.00
11:69641509:G:GT	donor_gain	1.00
11:69641508:GGAGG:G	donor_loss	0.99
11:69641510:AGG:A	donor_loss	0.99
11:69641511:GGTGC:G	donor_loss	0.99
11:69641512:GTGCG:G	donor_loss	0.99
11:69641513:T:A	donor_loss	0.99
11:69641484:G:GT	donor_gain	0.99
11:69641502:G:GT	donor_gain	0.96
11:69641535:T:TG	donor_gain	0.96
11:69641535:T:G	donor_gain	0.95
11:69641509:G:T	donor_gain	0.94
11:69641508:GGAG:G	donor_gain	0.94
11:69641509:GAG:G	donor_gain	0.93

Variant	Protein Change	AM Score	Classification
11:69641360:C:A	A16E	0.992	likely_pathogenic
11:69641332:T:C	C7R	0.980	likely_pathogenic
11:69641356:C:A	R15S	0.979	likely_pathogenic
11:69641334:C:G	C7W	0.973	likely_pathogenic
11:69641357:G:C	R15P	0.959	likely_pathogenic
11:69641332:T:A	C7S	0.959	likely_pathogenic
11:69641360:C:T	A16V	0.958	likely_pathogenic
11:69641333:G:A	C7Y	0.955	likely_pathogenic
11:69641333:G:C	C7S	0.959	likely_pathogenic
11:69641359:G:C	A16P	0.954	likely_pathogenic
11:69641339:A:T	E9V	0.953	likely_pathogenic
11:69641338:G:A	E9K	0.949	likely_pathogenic
11:69641359:G:A	A16T	0.924	likely_pathogenic
11:69641356:C:G	R15G	0.913	likely_pathogenic
11:69641339:A:C	E9A	0.895	likely_pathogenic
11:69641327:T:C	L5P	0.895	likely_pathogenic
11:69641327:T:A	L5H	0.880	likely_pathogenic
11:69641356:C:T	R15C	0.866	likely_pathogenic
11:69641333:G:T	C7F	0.864	likely_pathogenic
11:69641339:A:G	E9G	0.858	likely_pathogenic

Pathway ID	Name	Disease
R-HSA-69231	Cyclin D associated events in G1	No
R-HSA-75815	Ubiquitin-dependent degradation of Cyclin D	No
R-HSA-187577	SCF(Skp2)-mediated degradation of p27/p21	No
R-HSA-1912408	Pre-NOTCH Transcription and Translation	No
R-HSA-3214858	RMTs methylate histone arginines	No
R-HSA-6785807	Interleukin-4 and Interleukin-13 signaling	No
R-HSA-8849470	PTK6 Regulates Cell Cycle	No
R-HSA-8853884	Transcriptional Regulation by VENTX	No
R-HSA-8878166	Transcriptional regulation by RUNX2	No
R-HSA-8934593	Regulation of RUNX1 Expression and Activity	No
R-HSA-8951430	RUNX3 regulates WNT signaling	No
R-HSA-8951936	RUNX3 regulates p14-ARF	No
R-HSA-9018519	Estrogen-dependent gene expression	No
R-HSA-9634638	Estrogen-dependent nuclear events downstream of ESR-membrane signaling	No
R-HSA-9661069	Defective binding of RB1 mutants to E2F1,(E2F2, E2F3)	Yes
R-HSA-9754119	Drug-mediated inhibition of CDK4/CDK6 activity	No
R-HSA-9825892	Regulation of MITF-M-dependent genes involved in cell cycle and proliferation	No
R-HSA-9929491	SPOP-mediated proteasomal degradation of PD-L1(CD274)	No

GO ID	Term
GO:0000082	G1/S transition of mitotic cell cycle
GO:0000122	negative regulation of transcription by RNA polymerase II
GO:0000320	re-entry into mitotic cell cycle
GO:0006974	DNA damage response
GO:0007595	lactation
GO:0009410	response to xenobiotic stimulus
GO:0010039	response to iron ion
GO:0010165	response to X-ray
GO:0010971	positive regulation of G2/M transition of mitotic cell cycle
GO:0016055	Wnt signaling pathway
GO:0030182	neuron differentiation
GO:0030857	negative regulation of epithelial cell differentiation
GO:0030968	endoplasmic reticulum unfolded protein response
GO:0031571	mitotic G1 DNA damage checkpoint signaling
GO:0032026	response to magnesium ion
GO:0032355	response to estradiol
GO:0033197	response to vitamin E
GO:0033327	Leydig cell differentiation
GO:0033598	mammary gland epithelial cell proliferation
GO:0033601	positive regulation of mammary gland epithelial cell proliferation

GO ID	Term
GO:0003714	transcription corepressor activity
GO:0004672	protein kinase activity
GO:0016538	cyclin-dependent protein serine/threonine kinase regulator activity
GO:0019899	enzyme binding
GO:0019901	protein kinase binding
GO:0042826	histone deacetylase binding
GO:0043539	protein serine/threonine kinase activator activity
GO:0044877	protein-containing complex binding
GO:0061575	cyclin-dependent protein serine/threonine kinase activator activity
GO:0070064	proline-rich region binding

GO ID	Term
GO:0000307	cyclin-dependent protein kinase holoenzyme complex
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005737	cytoplasm
GO:0005815	microtubule organizing center
GO:0005829	cytosol
GO:0005923	bicellular tight junction
GO:0017053	transcription repressor complex
GO:0031965	nuclear membrane
GO:0097128	cyclin D1-CDK4 complex
GO:0097131	cyclin D1-CDK6 complex

UniProt	Gene	Score	Description
P11802	CDK4	999	Cyclin-dependent kinase 4
P24941	CDK2	998	Cyclin-dependent kinase 2
Q00534	CDK6	998	Cyclin-dependent kinase 6
P38936	CDKN1A	996	Cyclin-dependent kinase inhibitor 1 (p21)
P46527	CDKN1B	992	Cyclin-dependent kinase inhibitor 1B (p27)
P06493	CDK1	984	Cyclin-dependent kinase 1
P03372	ESR1	972	Estrogen receptor alpha
P10415	BCL2	958	Apoptosis regulator Bcl-2
P01106	MYC	951	Myc proto-oncogene protein
Q96S94	COP1	950	E3 ubiquitin-protein ligase
P42771	CDKN2A	947	Cyclin-dependent kinase inhibitor 2A (p16)
P04637	TP53	928	Cellular tumor antigen p53
P35222	CTNNB1	926	Beta-catenin
P31749	AKT1	919	Serine/threonine-protein kinase AKT1
P40763	STAT3	899	Signal transducer and activator of transcription 3
Q00987	MDM2	898	E3 ubiquitin-protein ligase Mdm2
P11142	HSPA8	891	Heat shock cognate 71 kDa protein
Q01094	E2F1	877	Transcription factor E2F1
P15056	BRAF	864	Serine/threonine-protein kinase B-raf
P04626	ERBB2	863	Receptor tyrosine-protein kinase erbB-2

Partner	Interaction Type	Confidence
CDK4	physical association	0.990
CDKN1A (p21)	physical association	0.960
CDKN1B (p27)	physical association	0.910
CDK6	direct interaction	0.880
CDK2	physical association	0.880
RB1	phosphorylation reaction	0.730
BRCA1	physical association	0.460
AR	direct interaction	0.540
FBXO31	physical association	0.580

UniProt	Top Similarity	Avg Similarity
P50756	1.0000	0.9802
Q91780	1.0000	0.9801
P24385 (self)	0.9999	0.9818
P25322	0.9999	0.9817
P39948	0.9999	0.9817
Q5R6J5	0.9999	0.9818
Q04827	0.9999	0.9810
P30280	0.9999	0.9814
Q8WNW2	0.9997	0.9810
Q64HP0	0.9997	0.9821

UniProt	Identity	Bitscore	Description
P50756	99.8%	825	Cyclin D1 (Bos taurus)
Q91780	99.8%	825	Cyclin D1 (Mus musculus)
P24385	99.3%	565	Cyclin D1 (self)
Q5R6J5	99.3%	564	Cyclin D1 (Pongo abelii)
P39948	99.0%	583	Cyclin D1
P25322	99.0%	583	Cyclin D1
Q8WNW2	98.3%	565	Cyclin D1
P30280	98.3%	572	Cyclin D2
Q04827	98.3%	573	Cyclin D1
Q0P5D3	98.3%	565	Cyclin D1

TF	Regulation	Confidence
ESR1	Activation	High
CTNNB1 (β-catenin)	Activation	High
MYC	Activation	High
E2F1	Activation	High
STAT3	Activation	High
JUN	Activation	High
FOS	Repression	High
CREB1	Unknown	High
EGR1	Activation	High
SP1	Activation	High
NOTCH1/RBPJ	Activation	High
GLI1	Activation	High
LEF1/TCF4	Activation	High
NF-κB (RELA/p65)	Activation	High
FOXO1	Repression	High
FOXO3	Repression	Low
HIF1A	Repression	High
AR	Unknown	High
BCL3	Activation	High
ATF2	Activation	High

Regulator	Effect	Mechanism
MYC	Up-regulates	Transcriptional regulation
CTNNB1	Up-regulates	Transcriptional regulation
ESR1	Up-regulates	Transcriptional regulation
GSK3B	Down-regulates	Phosphorylation (degradation)
DYRK1B	Down-regulates	Phosphorylation
FBXO31	Down-regulates	Ubiquitination
SKP2	Down-regulates	Ubiquitination
HACE1	Down-regulates	Ubiquitination
Palbociclib	Down-regulates	Chemical inhibition

Target	Effect	Evidence
MSI1	Activation	CollecTRI
NOTCH1	Up-regulates	SIGNOR
CDK4	Up-regulates (binding)	SIGNOR
Proliferation	Up-regulates	SIGNOR

ChEMBL ID	Target Name	Type
CHEMBL1907601	CDK4/cyclin D1	PROTEIN COMPLEX
CHEMBL2111455	CDK6/cyclin D1	PROTEIN COMPLEX
CHEMBL3610	G1/S-specific cyclin-D1	SINGLE PROTEIN
CHEMBL2095942	CDK4/cyclin D	PROTEIN COMPLEX GROUP
CHEMBL5483183	CDK6/Cyclin D	PROTEIN COMPLEX GROUP
CHEMBL3885551	CDK1/cyclin-D1	PROTEIN COMPLEX
CHEMBL3885552	CDK2/cyclin-D1	PROTEIN COMPLEX
CHEMBL4523688	CRBN/cyclin-D1	PROTEIN-PROTEIN INTERACTION

ChEMBL ID	Drug Name	Phase	Type
CHEMBL189963	PALBOCICLIB (Ibrance)	4 (Approved)	Small molecule
CHEMBL3545110	RIBOCICLIB (Kisqali)	4 (Approved)	Small molecule
CHEMBL3301610	ABEMACICLIB (Verzenio)	4 (Approved)	Small molecule
CHEMBL3894860	TRILACICLIB (Cosela)	4 (Approved)	Small molecule
CHEMBL2103840	DINACICLIB	3	Small molecule
CHEMBL3904602	LEROCICLIB	3	Small molecule
CHEMBL428690	ALVOCIDIB (Flavopiridol)	3	Small molecule
CHEMBL50	QUERCETIN	3	Small molecule

Field	Value
PharmGKB ID	PA75
Symbol	CCND1
VIP Gene	Yes
Has CPIC Guideline	No
Chromosome	chr11

Metric	Value
Expression Breadth	Ubiquitous
Total Present Calls	280
Total Absent Calls	15
Total Conditions	295
Max Expression Score	99.09
Average Expression Score	84.04
Gold Quality Count	270

Rank	Tissue/Condition	Expression Score	Quality
1	Endometrium epithelium	99.09	Gold
2	Stromal cell of endometrium	98.30	Gold
3	Upper arm skin	97.20	Gold
4	Esophagus squamous epithelium	97.00	Gold
5	Upper leg skin	96.62	Gold
6	Mucosa of paranasal sinus	96.57	Gold
7	Sural nerve	96.44	Gold
8	Epithelium of esophagus	96.30	Gold
9	Squamous epithelium	96.19	Gold
10	Gingival epithelium	96.07	Gold
11	Nipple	96.05	Gold
12	Lower esophagus mucosa	95.92	Gold
13	Tibia	95.86	Gold
14	Esophagus mucosa	95.42	Gold
15	Gingiva	95.38	Gold
16	Hair follicle	95.36	Gold
17	Skin of abdomen	95.32	Gold
18	Palpebral conjunctiva	95.04	Gold
19	Zone of skin	94.77	Gold
20	Right coronary artery	94.72	Gold
21	Oral cavity	94.50	Gold
22	Skin of leg	94.45	Gold
23	Cervix squamous epithelium	94.37	Silver
24	Penis	94.28	Gold
25	Caput epididymis	94.01	Gold
26	Skin of hip	93.86	Gold
27	Apex of heart	93.80	Gold
28	Prostate gland	93.65	Gold
29	Mammalian vulva	93.57	Gold
30	Ascending aorta	93.56	Gold

Experiment	Description	Cell Count
E-MTAB-10287	Endometrial biopsies	340,047
E-CURD-53	SARS-CoV infected cells	187,349
E-MTAB-8495	Human biliary tree	160,459
E-CURD-79	Human thymic development	152,320
E-MTAB-8894	Fetal ganglionic eminence	150,129
E-MTAB-6308	Lung tumor endothelial cells	113,132
E-CURD-120	Ankylosing spondylitis lymphocytes	62,428
E-MTAB-9435	Glioblastoma tumors	62,867
E-GEOD-125970	Human intestine	23,809
E-MTAB-10485	Neural progenitors	18,649

Orphanet ID	Disease	Type	Gene Count
ORPHA:29073	Multiple myeloma	Disease	1
ORPHA:52416	Mantle cell lymphoma	Disease	3
ORPHA:67038	B-cell chronic lymphocytic leukemia	Disease	10
ORPHA:892	Von Hippel-Lindau disease	Disease	2

HPO ID	Phenotype
HP:0006775	Multiple myeloma
HP:0012191	B-cell lymphoma
HP:0006716	Hereditary nonpolyposis colorectal carcinoma
HP:0003003	Colon cancer
HP:0005584	Renal cell carcinoma
HP:0002666	Pheochromocytoma
HP:0002668	Paraganglioma
HP:0006748	Adrenal pheochromocytoma
HP:0006880	Cerebellar hemangioblastoma
HP:0009713	Spinal hemangioblastoma
HP:0009711	Retinal capillary hemangioma
HP:0030393	Endolymphatic sac tumor
HP:0001737	Pancreatic cysts
HP:0008261	Pancreatic islet cell adenoma
HP:0005562	Multiple renal cysts
HP:0001638	Cardiomyopathy
HP:0001658	Myocardial infarction
HP:0012819	Myocarditis
HP:0001903	Anemia
HP:0001901	Polycythemia
HP:0002716	Lymphadenopathy
HP:0002797	Osteolysis
HP:0002756	Pathologic fracture
HP:0002953	Vertebral compression fracture
HP:0000938	Osteopenia
HP:0002653	Bone pain

Study ID	Trait	p-value
GCST004988_532	Breast cancer	4.0e-95
GCST004988_540	Breast cancer	6.0e-47
GCST010304_63	Cutaneous malignant melanoma	9.0e-21
GCST010303_55	Nevus count or melanoma	4.0e-18
GCST004412_6	Craniofacial microsomia	4.0e-17
GCST002346_17	Breast cancer (early onset)	2.0e-15
GCST000678_13	Breast cancer	3.0e-15
GCST007094_137	Diastolic blood pressure	2.0e-09
GCST90020028_464	Hip circumference adj. BMI	7.0e-15
GCST003061_6	Cutaneous malignant melanoma	2.0e-12
GCST004142_21	Melanoma	2.0e-12
GCST009379_270	Type 2 diabetes	5.0e-12
GCST002702_41	Height	1.0e-11
GCST008362_29	Birth weight	9.0e-12
GCST001906_21	Multiple myeloma (IgH translocation)	2.0e-11
GCST001906_1	Multiple myeloma (IgH translocation)	8.0e-11
GCST004028_5	AL amyloidosis	8.0e-11
GCST005348_3	Total body bone mineral density	4.0e-09
GCST010118_42	Type 2 diabetes	5.0e-09
GCST003985_8	Breast size	1.0e-09

Category	Count
Gene Identifiers	6 databases
Transcripts (Ensembl)	7
Protein Coding Transcripts	3
CCDS	1
Exons (canonical)	5
UniProt Entries	3
InterPro Domains	6
PDB Structures	11
Cross-Species Orthologs	15
ClinVar Variants	50
SpliceAI Predictions	854+
AlphaMissense Predictions	1,940
Reactome Pathways	18
GO Annotations	54
STRING Interactions	7,562
IntAct Interactions	196
ESM2 Similar Proteins	59
DIAMOND Homologs	40
Upstream TF Regulators	100+
SIGNOR Interactions	70
ChEMBL Targets	8
Approved Drugs (CDK4/6i)	4
Bgee Expression Conditions	295
Single-Cell Experiments	19
HPO Phenotypes	94
GWAS Associations	45
Orphanet Diseases	4
MSigDB Gene Sets	1,007