CARNS1

carnosine synthase 1

Basic information

Region (hg38): 11:67414968-67425607

Previous symbols: [ "ATPGD1" ]

Links

ENSG00000172508 ∙ NCBI:57571 ∙ OMIM:613368 ∙ HGNC:29268 ∙ Uniprot:A5YM72 ∙ 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 CARNS1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CARNS1 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			62	3		65
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	64	3	0

Variants in CARNS1

This is a list of pathogenic ClinVar variants found in the CARNS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-67417411-C-T		not specified	Uncertain significance (Apr 01, 2024)
11-67417440-T-G		not specified	Uncertain significance (Nov 06, 2023)
11-67417474-G-A		not specified	Uncertain significance (May 24, 2024)
11-67417501-C-T		not specified	Uncertain significance (May 17, 2023)
11-67417530-C-T		not specified	Uncertain significance (Oct 29, 2021)
11-67417568-G-C		not specified	Uncertain significance (Feb 23, 2023)
11-67417573-C-T		not specified	Uncertain significance (Aug 08, 2022)
11-67417581-C-T		not specified	Uncertain significance (Mar 20, 2024)
11-67417621-G-A		not specified	Uncertain significance (Jan 26, 2022)
11-67417630-A-G		not specified	Uncertain significance (Feb 27, 2023)
11-67417651-A-G		not specified	Uncertain significance (Feb 16, 2023)
11-67417657-G-T		not specified	Uncertain significance (Jul 13, 2022)
11-67418443-C-T		not specified	Uncertain significance (Oct 05, 2023)
11-67418825-C-T		not specified	Uncertain significance (Dec 18, 2023)
11-67418845-G-T		not specified	Uncertain significance (Jan 23, 2024)
11-67418848-G-T		not specified	Uncertain significance (Jan 24, 2024)
11-67418899-C-T		not specified	Uncertain significance (Mar 01, 2024)
11-67418902-C-T		not specified	Uncertain significance (Mar 19, 2024)
11-67418903-G-A		not specified	Uncertain significance (Jan 31, 2023)
11-67418911-T-C		not specified	Uncertain significance (Mar 14, 2023)
11-67418944-C-T		not specified	Uncertain significance (Dec 01, 2022)
11-67419014-G-A		not specified	Uncertain significance (Apr 01, 2024)
11-67419199-G-T		not specified	Uncertain significance (Dec 12, 2022)
11-67419229-G-A		not specified	Uncertain significance (Feb 07, 2023)
11-67419523-C-T		not specified	Uncertain significance (Feb 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CARNS1	protein_coding	protein_coding	ENST00000445895	9	10640

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000203	0.974	124599	0	61	124660	0.000245

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	397	459	0.865	0.0000296	5835
Missense in Polyphen		125	147.3	0.84861		1718
Synonymous	1.52	176	204	0.865	0.0000124	2162
Loss of Function	2.06	13	23.9	0.544	0.00000128	328

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000189
Ashkenazi Jewish	0.00	0.00
East Asian	0.000647	0.000612
Finnish	0.0000512	0.0000464
European (Non-Finnish)	0.000408	0.000363
Middle Eastern	0.000647	0.000612
South Asian	0.0000357	0.0000327
Other	0.000367	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the synthesis of carnosine and homocarnosine. Carnosine is synthesized more efficiently than homocarnosine. {ECO:0000269|PubMed:20097752}.
• Pathway: Arginine and proline metabolism - Homo sapiens (human);beta-Alanine metabolism - Homo sapiens (human);Histidine metabolism - Homo sapiens (human);Histidine Metabolism;Histidinemia;Histidine catabolism;Histidine, lysine, phenylalanine, tyrosine, proline and tryptophan catabolism;Metabolism of amino acids and derivatives;homocarnosine biosynthesis;Metabolism;carnosine biosynthesis (Consensus)

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.361
• ghis: 0.458

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Carns1

Gene ontology

• Biological process: histidine catabolic process;carnosine biosynthetic process
• Cellular component: cellular_component;cytosol
• Molecular function: ATP binding;FMN binding;ATPase activity;metal ion binding;carnosine synthase activity;homocarnosine synthase activity