CARNMT1

carnosine N-methyltransferase 1, the group of 7BS small molecule methyltransferases

Basic information

Region (hg38): 9:74980790-75028423

Previous symbols: [ "C9orf41" ]

Links

ENSG00000156017 ∙ NCBI:138199 ∙ OMIM:616552 ∙ HGNC:23435 ∙ Uniprot:Q8N4J0 ∙ 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 CARNMT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CARNMT1 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					1	1
missense			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	1

Variants in CARNMT1

This is a list of pathogenic ClinVar variants found in the CARNMT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-74983820-T-C		not specified	Uncertain significance (Nov 21, 2024)
9-74983843-G-A		not specified	Uncertain significance (Jun 13, 2023)
9-74984913-C-G		not specified	Uncertain significance (Apr 07, 2023)
9-74984975-C-T		not specified	Uncertain significance (Dec 28, 2022)
9-74984977-T-C		not specified	Uncertain significance (Jun 17, 2024)
9-74998614-C-G		not specified	Uncertain significance (Jan 24, 2025)
9-74998623-A-G			Benign (Oct 22, 2018)
9-74998646-T-C		not specified	Uncertain significance (Oct 01, 2024)
9-74998651-C-A		not specified	Uncertain significance (Mar 07, 2024)
9-74998760-T-G		not specified	Uncertain significance (May 14, 2024)
9-74998763-T-G		not specified	Uncertain significance (Sep 26, 2024)
9-74998766-T-C		not specified	Uncertain significance (Dec 18, 2023)
9-75016274-T-C		not specified	Uncertain significance (Nov 07, 2023)
9-75016275-C-G		not specified	Uncertain significance (Apr 03, 2023)
9-75016361-A-T		not specified	Uncertain significance (Feb 12, 2025)
9-75017313-T-C		not specified	Uncertain significance (May 13, 2022)
9-75017315-T-C		not specified	Uncertain significance (Dec 16, 2023)
9-75017328-A-T		not specified	Uncertain significance (Dec 30, 2024)
9-75017355-G-T		not specified	Uncertain significance (Jun 13, 2023)
9-75017357-G-A		not specified	Uncertain significance (Aug 13, 2021)
9-75017431-C-T		not specified	Uncertain significance (Aug 04, 2023)
9-75028012-C-T		Intellectual disability	Likely pathogenic (-)
9-75028054-C-T		not specified	Uncertain significance (Nov 28, 2023)
9-75028056-C-A		not specified	Uncertain significance (Aug 26, 2022)
9-75028058-C-G		not specified	Uncertain significance (Oct 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CARNMT1	protein_coding	protein_coding	ENST00000376834	8	47404

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00246	0.995	125724	0	16	125740	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.88	130	206	0.632	0.00000995	2677
Missense in Polyphen		27	66.179	0.40798		837
Synonymous	0.00506	67	67.1	0.999	0.00000297	750
Loss of Function	2.60	8	20.8	0.385	0.00000110	245

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000999	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000796	0.0000791
Middle Eastern	0.000109	0.000109
South Asian	0.0000667	0.0000653
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: N-methyltransferase that mediates the formation of anserine (beta-alanyl-N(Pi)-methyl-L-histidine) from carnosine. Anserine, a methylated derivative of carnosine (beta-alanyl-L- histidine), is an abundant constituent of vertebrate skeletal muscles. Also methylates other L-histidine-containing di- and tripeptides such as Gly-Gly-His, Gly-His and homocarnosine (GABA- His). {ECO:0000269|PubMed:26001783}.
• Pathway: Histidine metabolism - Homo sapiens (human);Histidine catabolism;Histidine, lysine, phenylalanine, tyrosine, proline and tryptophan catabolism;Metabolism of amino acids and derivatives;Metabolism (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• rvis_EVS: -0.3
• rvis_percentile_EVS: 32.62

Haploinsufficiency Scores

• pHI: 0.463
• hipred: Y
• hipred_score: 0.673
• ghis: 0.687

Essentials

• essential_gene_gene_trap: H

Mouse Genome Informatics

• Gene name: Carnmt1

Gene ontology

• Biological process: histidine catabolic process;methylation;carnosine metabolic process
• Cellular component: nucleus;cytosol
• Molecular function: S-adenosylmethionine-dependent methyltransferase activity;carnosine N-methyltransferase activity