PRMT7 (protein arginine methyltransferase 7)

Gene

• Entrez ID: 54496
• Gene name: Protein arginine methyltransferase 7
• Gene symbol: PRMT7
• Synonyms (NCBI Gene): SBIDDS
• Chromosome: 16
• Chromosome location: 16q22.1
• Summary: This gene encodes a member of the protein arginine N-methyltransferase family of proteins. The encoded enzyme transfers single methyl groups to arginine residues to generate monomethylarginines on histone proteins as well as other protein substrates. This

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs149170494	G>C	Pathogenic	Coding sequence variant, 5 prime UTR variant, non coding transcript variant, missense variant
rs201824659	G>T	Pathogenic	Splice acceptor variant
rs751670999	T>C	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs762515973	A>G	Pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs886039897	G>A	Pathogenic	Splice acceptor variant, intron variant
rs1014959895	G>C,T	Pathogenic, likely-pathogenic	Coding sequence variant, missense variant, stop gained, intron variant, non coding transcript variant
rs1251713297	C>A	Pathogenic	Non coding transcript variant, downstream transcript variant, stop gained, coding sequence variant, genic downstream transcript variant
rs1390386790	CT>-	Likely-pathogenic	Frameshift variant, non coding transcript variant, downstream transcript variant, genic downstream transcript variant, coding sequence variant
rs1567690011	AG>-	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1567721991	->GCTCTCCG	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant, intron variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT047476	hsa-miR-10b-5p	CLASH	23622248
MIRT046164	hsa-miR-30b-5p	CLASH	23622248
MIRT042041	hsa-miR-484	CLASH	23622248
MIRT535021	hsa-miR-6856-3p	PAR-CLIP	20371350
MIRT535020	hsa-miR-4323	PAR-CLIP	20371350
MIRT535019	hsa-miR-3943	PAR-CLIP	20371350
MIRT535018	hsa-miR-6849-3p	PAR-CLIP	20371350
MIRT570549	hsa-miR-361-3p	PAR-CLIP	20371350
MIRT570548	hsa-miR-3127-3p	PAR-CLIP	20371350
MIRT570547	hsa-miR-6756-3p	PAR-CLIP	20371350
MIRT535017	hsa-miR-766-3p	PAR-CLIP	20371350
MIRT535016	hsa-miR-5699-5p	PAR-CLIP	20371350
MIRT535015	hsa-miR-24-1-5p	PAR-CLIP	20371350
MIRT535014	hsa-miR-24-2-5p	PAR-CLIP	20371350
MIRT535013	hsa-miR-6778-3p	PAR-CLIP	20371350
MIRT535012	hsa-miR-6791-3p	PAR-CLIP	20371350
MIRT535011	hsa-miR-6829-3p	PAR-CLIP	20371350
MIRT535010	hsa-miR-6512-3p	PAR-CLIP	20371350
MIRT535009	hsa-miR-6720-5p	PAR-CLIP	20371350
MIRT535008	hsa-miR-5001-3p	PAR-CLIP	20371350
MIRT535007	hsa-miR-6836-3p	PAR-CLIP	20371350
MIRT535021	hsa-miR-6856-3p	PAR-CLIP	22012620
MIRT535020	hsa-miR-4323	PAR-CLIP	22012620
MIRT535019	hsa-miR-3943	PAR-CLIP	22012620
MIRT535018	hsa-miR-6849-3p	PAR-CLIP	22012620
MIRT535017	hsa-miR-766-3p	PAR-CLIP	22012620
MIRT535016	hsa-miR-5699-5p	PAR-CLIP	22012620
MIRT535015	hsa-miR-24-1-5p	PAR-CLIP	22012620
MIRT535014	hsa-miR-24-2-5p	PAR-CLIP	22012620
MIRT535013	hsa-miR-6778-3p	PAR-CLIP	22012620
MIRT535012	hsa-miR-6791-3p	PAR-CLIP	22012620
MIRT535011	hsa-miR-6829-3p	PAR-CLIP	22012620
MIRT535010	hsa-miR-6512-3p	PAR-CLIP	22012620
MIRT535009	hsa-miR-6720-5p	PAR-CLIP	22012620
MIRT535008	hsa-miR-5001-3p	PAR-CLIP	22012620
MIRT535007	hsa-miR-6836-3p	PAR-CLIP	22012620
MIRT449884	hsa-miR-656-3p	PAR-CLIP	22100165
MIRT449883	hsa-miR-7856-5p	PAR-CLIP	22100165
MIRT535021	hsa-miR-6856-3p	PAR-CLIP	20371350
MIRT535020	hsa-miR-4323	PAR-CLIP	20371350
MIRT535019	hsa-miR-3943	PAR-CLIP	20371350
MIRT535018	hsa-miR-6849-3p	PAR-CLIP	20371350
MIRT570549	hsa-miR-361-3p	PAR-CLIP	20371350
MIRT570548	hsa-miR-3127-3p	PAR-CLIP	20371350
MIRT570547	hsa-miR-6756-3p	PAR-CLIP	20371350
MIRT535017	hsa-miR-766-3p	PAR-CLIP	20371350
MIRT535016	hsa-miR-5699-5p	PAR-CLIP	20371350
MIRT535015	hsa-miR-24-1-5p	PAR-CLIP	20371350
MIRT535014	hsa-miR-24-2-5p	PAR-CLIP	20371350
MIRT535013	hsa-miR-6778-3p	PAR-CLIP	20371350
MIRT535012	hsa-miR-6791-3p	PAR-CLIP	20371350
MIRT535011	hsa-miR-6829-3p	PAR-CLIP	20371350
MIRT535010	hsa-miR-6512-3p	PAR-CLIP	20371350
MIRT535009	hsa-miR-6720-5p	PAR-CLIP	20371350
MIRT535008	hsa-miR-5001-3p	PAR-CLIP	20371350
MIRT535007	hsa-miR-6836-3p	PAR-CLIP	20371350
MIRT535021	hsa-miR-6856-3p	PAR-CLIP	22012620
MIRT535020	hsa-miR-4323	PAR-CLIP	22012620
MIRT535019	hsa-miR-3943	PAR-CLIP	22012620
MIRT535018	hsa-miR-6849-3p	PAR-CLIP	22012620
MIRT535017	hsa-miR-766-3p	PAR-CLIP	22012620
MIRT535016	hsa-miR-5699-5p	PAR-CLIP	22012620
MIRT535015	hsa-miR-24-1-5p	PAR-CLIP	22012620
MIRT535014	hsa-miR-24-2-5p	PAR-CLIP	22012620
MIRT535013	hsa-miR-6778-3p	PAR-CLIP	22012620
MIRT535012	hsa-miR-6791-3p	PAR-CLIP	22012620
MIRT535011	hsa-miR-6829-3p	PAR-CLIP	22012620
MIRT535010	hsa-miR-6512-3p	PAR-CLIP	22012620
MIRT535009	hsa-miR-6720-5p	PAR-CLIP	22012620
MIRT535008	hsa-miR-5001-3p	PAR-CLIP	22012620
MIRT535007	hsa-miR-6836-3p	PAR-CLIP	22012620
MIRT449884	hsa-miR-656-3p	PAR-CLIP	22100165
MIRT449883	hsa-miR-7856-5p	PAR-CLIP	22100165

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000387	Process	Spliceosomal snRNP assembly	IMP	17709427
GO:0001650	Component	Fibrillar center	IDA
GO:0005515	Function	Protein binding	IPI	28587924, 32296183, 33961781
GO:0005634	Component	Nucleus	IDA	15494416
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IDA	15494416
GO:0005829	Component	Cytosol	IEA
GO:0006325	Process	Chromatin organization	IEA
GO:0006338	Process	Chromatin remodeling	IBA
GO:0006355	Process	Regulation of DNA-templated transcription	IBA
GO:0008168	Function	Methyltransferase activity	IEA
GO:0008757	Function	S-adenosylmethionine-dependent methyltransferase activity	IDA	15044439
GO:0016274	Function	Protein-arginine N-methyltransferase activity	IBA
GO:0016274	Function	Protein-arginine N-methyltransferase activity	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0018216	Process	Peptidyl-arginine methylation	IMP	17709427
GO:0030154	Process	Cell differentiation	IEA
GO:0032259	Process	Methylation	IEA
GO:0035241	Function	Protein-arginine omega-N monomethyltransferase activity	IDA	15044439, 19110445
GO:0035241	Function	Protein-arginine omega-N monomethyltransferase activity	IEA
GO:0035243	Function	Protein-arginine omega-N symmetric methyltransferase activity	IDA	15494416, 19110445
GO:0035243	Function	Protein-arginine omega-N symmetric methyltransferase activity	IEA
GO:0035243	Function	Protein-arginine omega-N symmetric methyltransferase activity	IMP	17709427
GO:0042054	Function	Histone methyltransferase activity	IBA
GO:0042393	Function	Histone binding	IDA	15494416
GO:0043021	Function	Ribonucleoprotein complex binding	IPI	17709427
GO:0044020	Function	Histone H4R3 methyltransferase activity	IEA
GO:0044020	Function	Histone H4R3 methyltransferase activity	ISS
GO:0071514	Process	Genomic imprinting	IEA
GO:0071514	Process	Genomic imprinting	ISS
GO:0140939	Function	Histone H4 methyltransferase activity	IDA	15494416
GO:0140939	Function	Histone H4 methyltransferase activity	IEA

Other IDs

• MIM: 610087
• HGNC: 25557
• e!Ensembl: ENSG00000132600

Protein

• UniProt ID: Q9NVM4
• Protein name: Protein arginine N-methyltransferase 7 (EC 2.1.1.321) (Histone-arginine N-methyltransferase PRMT7) ([Myelin basic protein]-arginine N-methyltransferase PRMT7)
• Protein function: Arginine methyltransferase that can both catalyze the formation of omega-N monomethylarginine (MMA) and symmetrical dimethylarginine (sDMA), with a preference for the formation of MMA. Specifically mediates the symmetrical dimethylation of argin
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF06325	PrmA	54 → 149		Family

• Sequence:

  MKIFCSRANPTTGSVEWLEEDEHYDYHQEIARSSYADMLHDKDRNVKYYQGIRAAVSRVK
  DRGQKALVLDIGTGTGLLSMMAVTAGADFCYAIEVFKPMADAAVKIVEKNGFSDKIKVIN
  KHSTEVTVGPEGDMPCRANILVTELFDTELIGEGALPSYEHAHRHLVEENCEAVPHRATV
  YAQLVESGRMWSWNKLFPIHVQTSLGEQVIVPPVDVESCPGAPSVCDIQLNQVSPADFTV
  LSDVLPMFSIDFSKQVSSSAACHSRRFEPLTSGRAQVVLSWWDIEMDPEGKIKCTMAPFW
  AHSDPEEMQWRDHWMQCVYFLPQEEPVVQGSALYLVAHHDDYCVWYSLQRTSPEKNERVR
  QMRPVCDCQAHLLWNRPRFGEINDQDRTDRYVQALRTVLKPDSVCLCVSDGSLLSVLAHH
  LGVEQVFTVESSAASHKLLRKIFKANHLEDKINIIEKRPELLTNEDLQGRKVSLLLGEPF
  FTTSLLPWHNLYFWYVRTAVDQHLGPGAMVMPQAASLHAVVVEFRDLWRIRSPCGDCEGF
  DVHIMDDMIKRALDFRESREAEPHPLWEYPCRSLSEPWQILTFDFQQPVPLQPLCAEGTV
  ELRRPGQSHAAVLWMEYHLTPECTLSTGLLEPADPEGGCCWNPHCKQAVYFFSPAPDPRA
  LLGGPRTVSYAVEFHPDTGDIIMEFRHADTPD

• Sequence length: 692

Pathways

Reactome:

RMTs methylate histone arginines

Associated diseases

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
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Neurodevelopmental abnormality	Likely pathogenic; Pathogenic	rs201824659, rs2082897416	RCV001264712 RCV001264713	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
PRMT7-related disorder	Likely pathogenic; Pathogenic	rs201824659	RCV004754369	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Short stature-brachydactyly-obesity-global developmental delay syndrome	Pathogenic; Likely pathogenic	rs2151732301, rs1597361540, rs2151827144, rs2151436426, rs2151701931, rs2151558358, rs1313637057, rs1339009950, rs2545118734, rs886039897, rs149170494, rs762515973, rs201824659, rs2086255627, rs768950720, rs774937129, rs2545019503, rs2545046414, rs2545389934, rs1567690011, rs1567721991, rs1014959895, rs1251713297, rs372375423, rs1567739042, rs763953657	RCV001420150 RCV001420151 RCV001544514 RCV001784880 RCV001806400 RCV001813607 RCV002260535 RCV002260536 RCV002510670 RCV000256479 RCV000256464 RCV000256485 RCV000256436 RCV003324206 RCV003990839 RCV003995191 RCV004515767 RCV004555312 RCV004594846 RCV000681524 RCV000681525 RCV000763383 RCV006249661 RCV000709800 RCV001199929 RCV001199406	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
BRACHYDACTYLY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL HYPOPLASIA OF KIDNEY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EPILEPSY, PROGRESSIVE MYOCLONIC, 12	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Epileptic encephalopathy	Conflicting classifications of pathogenicity	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
HEPATOCELLULAR CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPERLIPIDEMIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OBESITY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SEVERE INTELLECTUAL DISABILITY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SKELETAL DYSPLASIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Acanthosis Nigricans	Acanthosis Nigricans	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Astigmatism	Astigmatism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Brachydactyly	Brachydactyly	BEFREE	27718516, 30006058		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Brachydactyly	Brachydactyly	Pubtator	36348013	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Brachydactyly	Brachydactyly	HPO_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Brachydactyly	Brachydactyly	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Brain Injuries Traumatic	Brain injuries	Pubtator	37196697	Associate	★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	25605249, 28188177, 31033288		★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	30699057, 33782401	Associate	★☆☆☆☆ Found in Text Mining only
Byzanthine arch palate	High palate	HPO_DG			★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	31732298, 35264579	Associate	★☆☆☆☆ Found in Text Mining only
Citrullinemia	Citrullinemia	BEFREE	28587924		★☆☆☆☆ Found in Text Mining only
Citrullinemia Type 1	Citrullinemia	BEFREE	28587924		★☆☆☆☆ Found in Text Mining only
Congenital Epicanthus	Congenital Epicanthus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital hypoplasia of kidney	Renal hypoplasia	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Dwarfism	Dwarfism	BEFREE	30006058		★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dwarfism Pituitary	Pituitary dwarfism	Pubtator	36348013	Associate	★☆☆☆☆ Found in Text Mining only
Frontal bossing	Frontal bossing	HPO_DG			★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Growth Disorders	Growth disorder	Pubtator	33270637, 36348013	Associate	★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	BEFREE	27718516, 30006058		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	25605249, 28188177, 31033288		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	28587924, 30802433		★☆☆☆☆ Found in Text Mining only
Mammary Neoplasms	Mammary Neoplasms	BEFREE	25605249		★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	BEFREE	27718516		★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Mitochondrial Diseases	Mitochondrial disease	Pubtator	37196697	Associate	★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	30147338		★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	HPO_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Obesity	Obesity	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Pseudohypoparathyroidism	Pseudohypoparathyroidism	BEFREE	30006058		★☆☆☆☆ Found in Text Mining only
Pseudohypoparathyroidism	Pseudohypoparathyroidism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Severe intellectual disability	Mental retardation	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SHORT STATURE, BRACHYDACTYLY, INTELLECTUAL DEVELOPMENTAL DISABILITY, AND SEIZURES	Short Stature, Brachydactyly, Intellectual Developmental Disability, And Seizures	ORPHANET_DG	26437029		★☆☆☆☆ Found in Text Mining only
SHORT STATURE, BRACHYDACTYLY, INTELLECTUAL DEVELOPMENTAL DISABILITY, AND SEIZURES	Short Stature, Brachydactyly, Intellectual Developmental Disability, And Seizures	UNIPROT_DG	26437029		★☆☆☆☆ Found in Text Mining only
SHORT STATURE, BRACHYDACTYLY, INTELLECTUAL DEVELOPMENTAL DISABILITY, AND SEIZURES	Short Stature, Brachydactyly, Intellectual Developmental Disability, And Seizures	GENOMICS_ENGLAND_DG	27718516		★☆☆☆☆ Found in Text Mining only
SHORT STATURE, BRACHYDACTYLY, INTELLECTUAL DEVELOPMENTAL DISABILITY, AND SEIZURES	Short Stature, Brachydactyly, Intellectual Developmental Disability, And Seizures	BEFREE	28902392		★☆☆☆☆ Found in Text Mining only
SHORT STATURE, BRACHYDACTYLY, INTELLECTUAL DEVELOPMENTAL DISABILITY, AND SEIZURES	Short Stature, Brachydactyly, Intellectual Developmental Disability, And Seizures	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Short stature-brachydactyly-obesity-global developmental delay syndrome	Short Stature, Brachydactyly, Intellectual Developmental Disability, And Seizures	Orphanet			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Skeletal dysplasia	Skeletal Dysplasia	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Steatohepatitis	Fatty Liver	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Strabismus	Strabismus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Thyroid Cancer Papillary	Papillary thyroid cancer	Pubtator	38092752	Associate	★☆☆☆☆ Found in Text Mining only