PCMTD1

protein-coding

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

Gene summary

Enables ubiquitin-like ligase-substrate adaptor activity. Involved in protein ubiquitination. Part of Cul5-RING ubiquitin ligase complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_052937.4

Inheritance

—

ClinVar variants

U:22

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.24

Max pathogenic AF

—

Genomic locus

chr8:51,817,575-51,899,186

External References & Databases

Ensembl (ENSG00000168300)

Transcript & Mutation Effects

hg38 • Region Span ~81.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PCMTD1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 20

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_052937.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			22 clinvar			22
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	22	0	0	22

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 42 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_052937.4	RefSeq	NP_443169.2	5	MANE Select
ENST00000522514.6	Ensembl	ENSP00000428099.1	5	MANE Select
NM_001286782.1	RefSeq	NP_001273711.1	4	Standard
NM_001286783.2	RefSeq	NP_001273712.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein methylation

Molecular Function

protein-L-isoaspartate (D-aspartate) O-methyltransferase activity

Cellular Component

cytoplasm
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000360540
Coding exons: 5
Length: 81596
Individuals with no LoFs: 125698
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125704
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.61	81	179	0.452	0.00000832	2331
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.107

Intolerance Scores

LoFtool: 0.848
RVIS EVS: 0.17
RVIS percentile EVS: 65.33

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.468

Gene Damage Prediction

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