COMTD1

catechol-O-methyltransferase domain containing 1, the group of 7BS small molecule methyltransferases

Basic information

Region (hg38): 10:75233641-75236030

Links

ENSG00000165644 ∙ NCBI:118881 ∙ ∙ HGNC:26309 ∙ Uniprot:Q86VU5 ∙ 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 COMTD1 gene.

• not_specified (38 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COMTD1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000144589.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			37	1		38
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	37	1	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COMTD1	protein_coding	protein_coding	ENST00000372538	7	2062

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000331	0.593	125533	0	57	125590	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.922	87	115	0.758	0.00000523	1569
Missense in Polyphen		24	35.431	0.67737		515
Synonymous	1.55	40	54.5	0.734	0.00000258	570
Loss of Function	0.750	8	10.6	0.752	4.97e-7	133

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00213	0.00160
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.000163	0.000139
European (Non-Finnish)	0.000111	0.000106
Middle Eastern	0.000381	0.000381
South Asian	0.000106	0.0000980
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative O-methyltransferase. {ECO:0000305}.

Recessive Scores

• pRec: 0.171

Haploinsufficiency Scores

• pHI: 0.236
• hipred: N
• hipred_score: 0.408
• ghis: 0.517

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.589

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Comtd1

Gene ontology

• Biological process: methylation
• Cellular component: integral component of membrane
• Molecular function: protein binding;O-methyltransferase activity;S-adenosylmethionine-dependent methyltransferase activity