PCMT1

protein-L-isoaspartate (D-aspartate) O-methyltransferase, the group of 7BS protein methyltransferases

Basic information

Region (hg38): 6:149749443-149811420

Links

ENSG00000120265 ∙ NCBI:5110 ∙ OMIM:176851 ∙ HGNC:8728 ∙ Uniprot:P22061 ∙ 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 PCMT1 gene.

• Inborn genetic diseases (6 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCMT1 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	6	1	0

Variants in PCMT1

This is a list of pathogenic ClinVar variants found in the PCMT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-149749761-G-T		not specified	Uncertain significance (Oct 27, 2021)
6-149749763-C-A		not specified	Uncertain significance (Dec 18, 2023)
6-149749795-C-T		not specified	Uncertain significance (Sep 22, 2023)
6-149749895-C-G		not specified	Uncertain significance (Aug 14, 2023)
6-149793634-C-A		not specified	Uncertain significance (Feb 03, 2022)
6-149793637-C-T		not specified	Uncertain significance (Nov 12, 2021)
6-149796457-A-G		not specified	Uncertain significance (Jan 04, 2022)
6-149802310-G-T		not specified	Uncertain significance (Sep 17, 2021)
6-149802334-C-T			Likely benign (Sep 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCMT1	protein_coding	protein_coding	ENST00000367384	8	61978

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.785	0.215	119988	0	1	119989	0.00000417

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.90	91	158	0.575	0.00000776	1834
Missense in Polyphen		9	51.428	0.175		603
Synonymous	-0.0199	62	61.8	1.00	0.00000319	569
Loss of Function	2.95	2	13.8	0.145	5.88e-7	180

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000298	0.0000298
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the methyl esterification of L-isoaspartyl and D-aspartyl residues in peptides and proteins that result from spontaneous decomposition of normal L-aspartyl and L-asparaginyl residues. It plays a role in the repair and/or degradation of damaged proteins. Acts on EIF4EBP2, microtubule-associated protein 2, calreticulin, clathrin light chains a and b, Ubiquitin carboxyl-terminal hydrolase isozyme L1, phosphatidylethanolamine- binding protein 1, stathmin, beta-synuclein and alpha-synuclein. {ECO:0000250|UniProtKB:P23506}.
• Pathway: Metabolism of proteins;Protein repair (Consensus)

Recessive Scores

• pRec: 0.177

Intolerance Scores

• loftool: 0.298
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.403
• hipred: Y
• hipred_score: 0.728
• ghis: 0.614

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 2.22e-16

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcmt1
• Phenotype: hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; immune system phenotype; muscle 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); growth/size/body region phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: protein methylation;protein repair
• Cellular component: cytoplasm;cytosol;extracellular exosome;extracellular vesicle
• Molecular function: protein-L-isoaspartate (D-aspartate) O-methyltransferase activity;protein binding;cadherin binding