PNMT

phenylethanolamine N-methyltransferase, the group of 7BS small molecule methyltransferases

Basic information

Region (hg38): 17:39667981-39670475

Previous symbols: [ "PENT" ]

Links

ENSG00000141744 ∙ NCBI:5409 ∙ OMIM:171190 ∙ HGNC:9160 ∙ Uniprot:P11086 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PNMT 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					1	1
missense			19	1	1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	2

Variants in PNMT

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

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

Position	Type	Phenotype	Significance	ClinVar
17-39668485-G-A		not specified	Uncertain significance (Apr 23, 2024)
17-39668537-C-A		not specified	Uncertain significance (Apr 23, 2024)
17-39668545-G-T		not specified	Uncertain significance (Oct 25, 2023)
17-39668584-C-T		not specified	Uncertain significance (Jan 19, 2024)
17-39668585-G-T		not specified	Uncertain significance (Jul 02, 2024)
17-39668597-C-T		not specified	Uncertain significance (Jul 09, 2021)
17-39668598-G-A			Benign (Apr 24, 2018)
17-39668609-G-C		not specified	Uncertain significance (Dec 15, 2022)
17-39668617-T-C		not specified	Uncertain significance (Nov 10, 2022)
17-39668651-G-A		not specified	Uncertain significance (Dec 18, 2023)
17-39669637-T-G		not specified	Uncertain significance (May 30, 2023)
17-39669643-C-T		not specified	Uncertain significance (May 27, 2022)
17-39669647-C-T		not specified	Uncertain significance (Dec 27, 2023)
17-39669650-T-C		not specified	Uncertain significance (Sep 04, 2024)
17-39669676-G-A		not specified	Uncertain significance (Jun 09, 2022)
17-39669677-T-C		not specified	Uncertain significance (Jan 10, 2022)
17-39669724-A-G		not specified	Uncertain significance (Jan 16, 2024)
17-39669781-G-C		not specified	Uncertain significance (Sep 22, 2023)
17-39669795-G-C		not specified	Uncertain significance (Jun 06, 2023)
17-39669812-A-G		not specified	Uncertain significance (Dec 14, 2023)
17-39670012-G-A		not specified	Uncertain significance (Dec 03, 2024)
17-39670018-C-T		not specified	Uncertain significance (Jul 06, 2021)
17-39670063-G-A			Benign (Jul 20, 2018)
17-39670159-C-T		not specified	Uncertain significance (Sep 12, 2023)
17-39670213-G-T		not specified	Uncertain significance (Dec 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PNMT	protein_coding	protein_coding	ENST00000269582	3	2495

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00501	0.896	125679	0	56	125735	0.000223

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.449	157	174	0.904	0.0000102	1777
Missense in Polyphen		63	74.172	0.84938		810
Synonymous	0.626	67	73.8	0.907	0.00000428	591
Loss of Function	1.41	5	9.73	0.514	5.01e-7	96

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000465	0.000456
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000608	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000371	0.000360
Middle Eastern	0.0000608	0.0000544
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Converts noradrenaline to adrenaline.
• Pathway: Tyrosine metabolism - Homo sapiens (human);Tyrosine hydroxylase deficiency;Tyrosinemia, transient, of the newborn;Dopamine beta-hydroxylase deficiency;Disulfiram Action Pathway;Tyrosine Metabolism;Alkaptonuria;Monoamine oxidase-a deficiency (MAO-A);Hawkinsinuria;Tyrosinemia Type I;Catecholamine Biosynthesis;Aromatic L-Aminoacid Decarboxylase Deficiency;Amino Acid metabolism;Biogenic Amine Synthesis;Methylation Pathways;Metabolism of amino acids and derivatives;Metabolism;catecholamine biosynthesis;Catecholamine biosynthesis;Tyrosine metabolism;noradrenaline and adrenaline degradation;Amine-derived hormones (Consensus)

Recessive Scores

• pRec: 0.333

Intolerance Scores

• loftool: 0.674
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.74

Haploinsufficiency Scores

• pHI: 0.444
• hipred: N
• hipred_score: 0.251
• ghis: 0.391

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.958

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pnmt
• Phenotype: normal phenotype; 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); 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); homeostasis/metabolism phenotype

Gene ontology

• Biological process: methylation;epinephrine biosynthetic process;catecholamine biosynthetic process
• Cellular component: cytoplasm;cytosol
• Molecular function: phenylethanolamine N-methyltransferase activity