PCMTD2

protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2, the group of 7BS protein methyltransferases

Basic information

Region (hg38): 20:64255694-64304820

Previous symbols: [ "C20orf36" ]

Links

ENSG00000203880 ∙ NCBI:55251 ∙ OMIM:620077 ∙ HGNC:15882 ∙ Uniprot:Q9NV79 ∙ 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 PCMTD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCMTD2 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						0
missense			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	0

Variants in PCMTD2

This is a list of pathogenic ClinVar variants found in the PCMTD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-64260039-G-A		not specified	Uncertain significance (Jul 12, 2022)
20-64260162-C-T		not specified	Uncertain significance (Jan 23, 2024)
20-64260200-C-G		not specified	Uncertain significance (Jan 17, 2023)
20-64265332-G-A		not specified	Uncertain significance (Jun 16, 2024)
20-64267914-T-G		not specified	Uncertain significance (Mar 25, 2024)
20-64267987-G-A		not specified	Uncertain significance (Nov 18, 2023)
20-64273262-G-A		not specified	Uncertain significance (Sep 14, 2023)
20-64273304-G-T		not specified	Uncertain significance (Mar 24, 2023)
20-64273316-G-A		not specified	Uncertain significance (May 02, 2024)
20-64273362-G-A		not specified	Uncertain significance (Feb 27, 2023)
20-64273425-A-G		not specified	Uncertain significance (Oct 14, 2023)
20-64273445-T-C		not specified	Uncertain significance (Apr 17, 2023)
20-64273446-G-T		not specified	Uncertain significance (Apr 17, 2023)
20-64273491-C-T		not specified	Likely benign (Jan 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCMTD2	protein_coding	protein_coding	ENST00000308824	5	39762

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00799	0.979	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.52	151	213	0.707	0.0000126	2355
Missense in Polyphen		32	61.976	0.51633		640
Synonymous	0.679	69	76.6	0.901	0.00000424	706
Loss of Function	2.18	6	15.2	0.396	9.01e-7	182

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.00	0.00
South Asian	0.000168	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.747
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.75

Haploinsufficiency Scores

• pHI: 0.182
• hipred: Y
• hipred_score: 0.603
• ghis: 0.634

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.251

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcmtd2

Gene ontology

• Biological process: protein methylation
• Cellular component: cytoplasm
• Molecular function: protein-L-isoaspartate (D-aspartate) O-methyltransferase activity