PCMTD1

protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1, the group of 7BS protein methyltransferases

Basic information

Region (hg38): 8:51817574-51899186

Links

ENSG00000168300 ∙ NCBI:115294 ∙ OMIM:620091 ∙ HGNC:30483 ∙ Uniprot:Q96MG8 ∙ 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 PCMTD1 gene.

• Inborn genetic diseases (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCMTD1 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in PCMTD1

This is a list of pathogenic ClinVar variants found in the PCMTD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-51820406-T-A		not specified	Uncertain significance (Aug 22, 2023)
8-51820644-C-G		not specified	Uncertain significance (Oct 14, 2023)
8-51820683-G-A		not specified	Uncertain significance (Jan 26, 2023)
8-51831473-T-A		not specified	Uncertain significance (Jun 09, 2022)
8-51831512-G-T		not specified	Uncertain significance (May 17, 2023)
8-51845702-T-G		not specified	Uncertain significance (Feb 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCMTD1	protein_coding	protein_coding	ENST00000360540	5	81596

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.267	0.732	125698	0	6	125704	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.61	81	179	0.452	0.00000832	2331
Missense in Polyphen		13	54.038	0.24057		661
Synonymous	1.12	47	57.9	0.812	0.00000264	615
Loss of Function	2.85	4	16.5	0.242	9.36e-7	207

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000474	0.0000462
European (Non-Finnish)	0.0000441	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.848
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.33

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.466
• ghis: 0.474

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.468

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcmtd1

Gene ontology

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