PRMT7

protein arginine methyltransferase 7, the group of 7BS protein arginine methyltranferases

Basic information

Region (hg38): 16:68310951-68360852

Links

ENSG00000132600 ∙ NCBI:54496 ∙ OMIM:610087 ∙ HGNC:25557 ∙ Uniprot:Q9NVM4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• short stature-brachydactyly-obesity-global developmental delay syndrome (Supportive), mode of inheritance: AR
• short stature-brachydactyly-obesity-global developmental delay syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Short stature, brachydactyly, intellectual developmental disability, and seizures	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed mediCONDITIONScal decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	26437029

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PRMT7 gene.

• Short stature-brachydactyly-obesity-global developmental delay syndrome (8 variants)
• not provided (2 variants)
• 15 conditions (1 variants)
• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRMT7 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				43	9	52
missense	1	3	83	6		93
nonsense	6	3				9
start loss						0
frameshift	5	5				10
inframe indel			2			2
splice donor/acceptor (+/-2bp)		3	1			4
splice region			9	9	2	20
non coding				17	7	24
Total	12	14	86	66	16

Highest pathogenic variant AF is 0.00000657

Variants in PRMT7

This is a list of pathogenic ClinVar variants found in the PRMT7 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
16-68311097-C-T		not specified	Likely benign (Jan 06, 2020)
16-68312039-C-G		Short stature-brachydactyly-obesity-global developmental delay syndrome	Uncertain significance (Sep 23, 2021)
16-68315896-G-A			Uncertain significance (Dec 21, 2022)
16-68316008-C-T			Uncertain significance (Dec 11, 2023)
16-68316055-TA-T			Pathogenic (Jul 03, 2019)
16-68316068-T-C		Inborn genetic diseases	Uncertain significance (Feb 12, 2024)
16-68316074-G-C		Short stature-brachydactyly-obesity-global developmental delay syndrome	Pathogenic (Jul 03, 2020)
16-68321410-CTT-C			Likely benign (Jul 24, 2023)
16-68321428-C-A		Short stature-brachydactyly-obesity-global developmental delay syndrome	Pathogenic (Oct 16, 2019)
16-68321466-A-C			Uncertain significance (Jan 18, 2024)
16-68321480-CTAT-C			Benign (May 05, 2023)
16-68324689-A-C		Inborn genetic diseases	Uncertain significance (Nov 22, 2021)
16-68324698-C-T		Neurodevelopmental abnormality	Pathogenic (Jun 04, 2020)
16-68324706-C-G		not specified	Uncertain significance (May 17, 2024)
16-68324707-C-T		Inborn genetic diseases	Uncertain significance (Apr 23, 2024)
16-68324714-C-T		not specified	Uncertain significance (May 17, 2024)
16-68324716-G-A		Inborn genetic diseases	Uncertain significance (Aug 12, 2021)
16-68324762-T-TTGGCAC			Uncertain significance (Sep 08, 2023)
16-68324772-C-T			Likely benign (Jan 01, 2024)
16-68324774-C-T		Epileptic encephalopathy	Likely pathogenic (Jun 12, 2020)
16-68324786-C-T		PRMT7-related disorder	Uncertain significance (May 12, 2023)
16-68324804-C-A		Short stature-brachydactyly-obesity-global developmental delay syndrome	Uncertain significance (Jan 14, 2022)
16-68324807-G-T		Inborn genetic diseases	Uncertain significance (Jun 27, 2022)
16-68324809-G-A			Uncertain significance (May 09, 2022)
16-68324811-C-T			Likely benign (Jun 06, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRMT7	protein_coding	protein_coding	ENST00000339507	17	47590

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.50e-15	0.536	125656	0	92	125748	0.000366

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.683	386	426	0.907	0.0000261	4550
Missense in Polyphen		80	107.92	0.74132		1117
Synonymous	-0.734	190	178	1.07	0.0000122	1313
Loss of Function	1.62	28	38.9	0.720	0.00000192	417

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000568	0.000567
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000275	0.000272
Finnish	0.000102	0.0000924
European (Non-Finnish)	0.000503	0.000501
Middle Eastern	0.000275	0.000272
South Asian	0.000301	0.000294
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: 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 arginine residues in the small nuclear ribonucleoproteins Sm D1 (SNRPD1) and Sm D3 (SNRPD3); such methylation being required for the assembly and biogenesis of snRNP core particles. Specifically mediates the symmetric dimethylation of histone H4 'Arg-3' to form H4R3me2s. Plays a role in gene imprinting by being recruited by CTCFL at the H19 imprinted control region (ICR) and methylating histone H4 to form H4R3me2s, possibly leading to recruit DNA methyltransferases at these sites. May also play a role in embryonic stem cell (ESC) pluripotency. Also able to mediate the arginine methylation of histone H2A and myelin basic protein (MBP) in vitro; the relevance of such results is however unclear in vivo. {ECO:0000269|PubMed:15044439, ECO:0000269|PubMed:15494416, ECO:0000269|PubMed:17709427, ECO:0000269|PubMed:19110445}.
• Disease: DISEASE: Short stature, brachydactyly, intellectual developmental disability, and seizures (SBIDDS) [MIM:617157]: An autosomal recessive disease characterized by developmental delay, learning disabilities, mild mental retardation, delayed speech, and skeletal abnormalities. Skeletal features include short stature, brachydactyly, and short metacarpals and metatarsals. {ECO:0000269|PubMed:26437029}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: RMTs methylate histone arginines;Chromatin modifying enzymes;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.663
• rvis_EVS: -1.9
• rvis_percentile_EVS: 1.95

Haploinsufficiency Scores

• pHI: 0.0472
• hipred: Y
• hipred_score: 0.545
• ghis: 0.587

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.924

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Prmt7
• Phenotype: neoplasm; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; liver/biliary system phenotype; embryo phenotype; skeleton phenotype; immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); endocrine/exocrine gland phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: spliceosomal snRNP assembly;regulation of gene expression by genetic imprinting;regulation of transcription, DNA-templated;histone methylation;peptidyl-arginine methylation;peptidyl-arginine methylation, to symmetrical-dimethyl arginine;peptidyl-arginine methylation, to asymmetrical-dimethyl arginine;cell differentiation;histone arginine methylation;DNA methylation involved in gamete generation;regulation of protein binding;histone H4-R3 methylation
• Cellular component: fibrillar center;nucleus;nucleoplasm;cytosol
• Molecular function: histone-arginine N-methyltransferase activity;S-adenosylmethionine-dependent methyltransferase activity;protein-arginine N-methyltransferase activity;[myelin basic protein]-arginine N-methyltransferase activity;protein-arginine omega-N monomethyltransferase activity;protein-arginine omega-N asymmetric methyltransferase activity;protein-arginine omega-N symmetric methyltransferase activity;histone binding;ribonucleoprotein complex binding;histone methyltransferase activity (H4-R3 specific)