CARNMT1

protein-coding

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

Gene summary

The protein encoded by this gene is a methyltransferase that converts carnosine to anserine, a dipeptide found abundantly in skeletal muscle. The encoded protein can methylate other dipeptides as well. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]

Previous symbols:

C9orf41

MANE transcript

NM_152420.3

Inheritance

—

ClinVar variants

P:1U:53B:2

Top phenotype

Intellectual disability

gnomAD constraint

pLI —, LoF o/e 0.39

Max pathogenic AF

—

Genomic locus

chr9:74,980,790-75,028,423

External References & Databases

Ensembl (ENSG00000156017)

Transcript & Mutation Effects

hg38 • Region Span ~47.6 kb

Loading mutation effect viewer...

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 CARNMT1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 49

not providedTotal: 1

Intellectual disabilityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152420.3. 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				1 clinvar	1 clinvar	2
missense		1 clinvar	50 clinvar			51
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	1	53	1	1	56

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152420.3	RefSeq	NP_689633.1	8	MANE Select
ENST00000376834.8	Ensembl	ENSP00000366030.3	8	MANE Select
NM_001320497.2	RefSeq	NP_001307426.1	7	Standard
ENST00000376830.3	Ensembl	ENSP00000366026.3	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Histidine metabolism - Homo sapiens (human)
Histidine catabolism
Histidine, lysine, phenylalanine, tyrosine, proline and tryptophan catabolism
Metabolism of amino acids and derivatives
Metabolism

Biological Process

histidine catabolic process
methylation
carnosine metabolic process

Molecular Function

S-adenosylmethionine-dependent methyltransferase activity
carnosine N-methyltransferase activity

Cellular Component

nucleus
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000376834
Coding exons: 8
Length: 47404
Individuals with no LoFs: 125724
Homozygous LoFs: 0
Heterozygous LoFs: 16
Defined: 125740
p: 0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.88	130	206	0.632	0.00000995	2677
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000080	0.000079	rare
South Asian	0.000067	0.000065	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.113

Intolerance Scores

RVIS EVS: -0.3
RVIS percentile EVS: 32.62

Essentials

Essential (gene trap): H