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.

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.

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			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	0

Variants in COMTD1

This is a list of pathogenic ClinVar variants found in the COMTD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-75234179-G-T		not specified	Likely benign (May 17, 2023)
10-75234192-T-G		not specified	Uncertain significance (Jul 25, 2023)
10-75234632-C-T		not specified	Uncertain significance (Oct 16, 2023)
10-75234681-C-T		not specified	Uncertain significance (Aug 02, 2021)
10-75234690-C-T		not specified	Uncertain significance (May 18, 2023)
10-75234739-C-G		not specified	Uncertain significance (Jan 27, 2025)
10-75234955-G-T		not specified	Uncertain significance (Nov 12, 2024)
10-75235121-C-A		not specified	Uncertain significance (Mar 01, 2024)
10-75235121-C-G		not specified	Uncertain significance (Dec 15, 2023)
10-75235130-G-A		not specified	Uncertain significance (Jan 17, 2023)
10-75235136-A-T		not specified	Uncertain significance (Aug 20, 2024)
10-75235170-T-C		not specified	Uncertain significance (Nov 13, 2023)
10-75235178-C-A		not specified	Uncertain significance (Oct 28, 2024)
10-75235269-A-G		not specified	Uncertain significance (Aug 05, 2024)
10-75235318-G-A		not specified	Uncertain significance (Jan 18, 2025)
10-75235323-G-C		not specified	Uncertain significance (Oct 10, 2023)
10-75235342-T-C		not specified	Uncertain significance (Aug 28, 2024)
10-75235651-T-A		not specified	Uncertain significance (Sep 25, 2024)
10-75235656-C-T		not specified	Uncertain significance (Mar 03, 2025)
10-75235657-G-C		not specified	Uncertain significance (Sep 25, 2024)
10-75235693-G-A		not specified	Uncertain significance (Mar 12, 2024)
10-75235716-C-G		not specified	Uncertain significance (May 08, 2023)
10-75235717-G-A		not specified	Uncertain significance (Jan 08, 2025)
10-75235901-C-T		not specified	Uncertain significance (Jan 20, 2025)
10-75235919-G-T		not specified	Uncertain significance (Oct 03, 2022)

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