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.

• not_specified (40 variants)
• not_provided (1 variants)
• Intellectual_disability (1 variants)

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. These statistics are base on transcript: NM_000152420.3. 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				1	1	2
missense		1	39			40
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	1	39	1	1

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