Gene Gene information from NCBI Gene database.
Entrez ID 63976
Gene name PR/SET domain 16
Gene symbol PRDM16
Synonyms (NCBI Gene)
CMD1LLKMT8FLVNC8MEL1PFM13
Chromosome 1
Chromosome location 1p36.32
Summary The reciprocal translocation t(1;3)(p36;q21) occurs in a subset of myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). This gene is located near the 1p36.3 breakpoint and has been shown to be specifically expressed in the t(1:3)(p36,q21)-posi
SNPs SNP information provided by dbSNP.
17
SNP ID Visualize variation Clinical significance Consequence
rs201517837 G>C Conflicting-interpretations-of-pathogenicity, likely-benign Intron variant
rs201517929 G>A Conflicting-interpretations-of-pathogenicity Missense variant, coding sequence variant
rs202115331 T>C Pathogenic Missense variant, coding sequence variant
rs368409902 G>A Conflicting-interpretations-of-pathogenicity Intron variant
rs374365034 G>A,T Conflicting-interpretations-of-pathogenicity Intron variant
miRNA miRNA information provided by mirtarbase database.
239
miRTarBase ID miRNA Experiments Reference
MIRT007382 hsa-miR-133b Luciferase reporter assay 23395168
MIRT007383 hsa-miR-133a-3p Luciferase reporter assay 23395168
MIRT027926 hsa-miR-96-5p Sequencing 20371350
MIRT046957 hsa-miR-221-3p CLASH 23622248
MIRT042704 hsa-miR-346 CLASH 23622248
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
51
GO ID Ontology Definition Evidence Reference
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IDA 19049980
GO:0000976 Function Transcription cis-regulatory region binding IDA 12816872
GO:0000978 Function RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
GO:0001227 Function DNA-binding transcription repressor activity, RNA polymerase II-specific IDA 12816872
GO:0001228 Function DNA-binding transcription activator activity, RNA polymerase II-specific IBA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
605557 14000 ENSG00000142611
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q9HAZ2
Protein name Histone-lysine N-methyltransferase PRDM16 (EC 2.1.1.367) (PR domain zinc finger protein 16) (PR domain-containing protein 16) (Transcription factor MEL1) (MDS1/EVI1-like gene 1)
Protein function Binds DNA and functions as a transcriptional regulator (PubMed:12816872). Displays histone methyltransferase activity and monomethylates 'Lys-9' of histone H3 (H3K9me1) in vitro (By similarity). Probably catalyzes the monomethylation of free his
PDB 2N1I , 6BW4
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF13912 zf-C2H2_6 229 251 Domain
PF00096 zf-C2H2 281 303 Zinc finger, C2H2 type Domain
PF00096 zf-C2H2 309 331 Zinc finger, C2H2 type Domain
PF00096 zf-C2H2 337 360 Zinc finger, C2H2 type Domain
PF00096 zf-C2H2 366 388 Zinc finger, C2H2 type Domain
PF00096 zf-C2H2 394 416 Zinc finger, C2H2 type Domain
PF00096 zf-C2H2 423 444 Zinc finger, C2H2 type Domain
PF00096 zf-C2H2 951 973 Zinc finger, C2H2 type Domain
PF00096 zf-C2H2 979 1002 Zinc finger, C2H2 type Domain
PF00096 zf-C2H2 1008 1030 Zinc finger, C2H2 type Domain
Tissue specificity TISSUE SPECIFICITY: Expressed in uterus and kidney. Expressed in both cardiomyocytes and interstitial cells. {ECO:0000269|PubMed:11050005, ECO:0000269|PubMed:12816872, ECO:0000269|PubMed:23768516}.
Sequence
MRSKARARKLAKSDGDVVNNMYEPNRDLLASHSAEDEAEDSAMSPIPVGPPSPFPTSEDF
TPKEGSPYEAPVYIPEDIPIPADFELRESSIPGAGLGVWAKRKMEAGERLGPCVVVPRAA
AKETDFGWEQILTDVEVSPQEGCITKISEDLGSEKFCVDANQAGAGSWLKYIRVACSCDD
QNLTMCQISEQIYYKVIKDIEPGEELLVHVKEGVYPLGTVPPGLDEEPTFRCDECDELFQ
SKLDLRRHKKY
TCGSVGAALYEGLAEELKPEGLGGGSGQAHECKDCERMFPNKYSLEQHM
VIH
TEEREYKCDQCPKAFNWKSNLIRHQMSHDSGKRFECENCVKVFTDPSNLQRHIRSQH
VGARAHACPDCGKTFATSSGLKQHKHIHSTVKPFICEVCHKSYTQFSNLCRHKRMHADCR
TQIKCKDCGQMFSTTSSLNKHRRFCEGKNHYTPGGIFAPGLPLTPSPMMDKAKPSPSLNH
ASLGFNEYFPSRPHPGSLPFSTAPPTFPALTPGFPGIFPPSLYPRPPLLPPTSLLKSPLN
HTQDAKLPSPLGNPALPLVSAVSNSSQGTTAAAGPEEKFESRLEDSCVEKLKTRSSDMSD
GSDFEDVNTTTGTDLDTTTGTGSDLDSDVDSDPDKDKGKGKSAEGQPKFGGGLAPPGAPN
SVAEVPVFYSQHSFFPPPDEQLLTATGAAGDSIKAIASIAEKYFGPGFMGMQEKKLGSLP
YHSAFPFQFLPNFPHSLYPFTDRALAHNLLVKAEPKSPRDALKVGGPSAECPFDLTTKPK
DVKPILPMPKGPSAPASGEEQPLDLSIGSRARASQNGGGREPRKNHVYGERKLGAGEGLP
QVCPARMPQQPPLHYAKPSPFFMDPIYSRVEKRKVTDPVGALKEKYLRPSPLLFHPQMSA
IETMTEKLESFAAMKADSGSSLQPLPHHPFNFRSPPPTLSDPILRKGKERYTCRYCGKIF
PRSANLTRHLRTH
TGEQPYRCKYCDRSFSISSNLQRHVRNIHNKEKPFKCHLCNRCFGQQ
TNLDRHLKKH
EHENAPVSQHPGVLTNHLGTSASSPTSESDNHALLDEKEDSYFSEIRNFI
ANSEMNQASTRTEKRADMQIVDGSAQCPGLASEKQEDVEEEDDDDLEEDDEDSLAGKSQD
DTVSPAPEPQAAYEDEEDEEPAASLAVGFDHTRRCAEDHEGGLLALEPMPTFGKGLDLRR
AAEEAFEVKDVLNSTLDSEALKHTLCRQAKNQAYAMMLSLSEDTPLHTPSQGSLDAWLKV
TGATSESGAFHPINHL
Sequence length 1276
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Lysine degradation
Metabolic pathways
Thermogenesis
  PKMTs methylate histone lysines
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
48
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Cardiomyopathy, dilated, 1LL Pathogenic rs202115331 RCV000054523
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Left ventricular noncompaction 8 Pathogenic; Likely pathogenic rs1643176372, rs2523887339, rs2523951441, rs2100664124, rs397514742, rs886041395 RCV001331228
RCV002290369
RCV003333648
RCV003985225
RCV000054518
View all (1 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Left ventricular noncompaction cardiomyopathy Pathogenic rs2100662912, rs397514742, rs886041395 RCV002204525
RCV002054880
RCV002295279
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
PRDM16-related congenital heart disease Likely pathogenic rs2523951441 RCV003492869
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
1P36 DELETION SYNDROME Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ASTHMA GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CARDIOMYOPATHY, DILATED Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CARDIOMYOPATHY, HYPERTROPHIC, FAMILIAL Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
1p36 deletion syndrome 1p36 deletion syndrome Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Abdominal Migraine Abdominal Migraine CTD_human_DG 21666692
★☆☆☆☆
Found in Text Mining only
Acute Confusional Migraine Confusional Migraine CTD_human_DG 21666692
★☆☆☆☆
Found in Text Mining only
Acute lymphocytic leukemia Lymphocytic Leukemia BEFREE 18202228
★☆☆☆☆
Found in Text Mining only
Acute monocytic leukemia Monocytic Leukemia BEFREE 12816872
★☆☆☆☆
Found in Text Mining only
Acute myelomonocytic leukemia Myelomonocytic Leukemia BEFREE 12557231
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of lung (disorder) Lung adenocarcinoma BEFREE 30132554, 30683132
★☆☆☆☆
Found in Text Mining only
Adult Acute Myeloblastic Leukemia Myeloblastic Leukemia BEFREE 28710806
★☆☆☆☆
Found in Text Mining only
Adult T-Cell Lymphoma/Leukemia T-Cell Lymphoma/Leukemia LHGDN 14656887
★☆☆☆☆
Found in Text Mining only
Agenesis of corpus callosum Agenesis Of Corpus Callosum HPO_DG
★☆☆☆☆
Found in Text Mining only