CNDP1

carnosine dipeptidase 1, the group of M20 metallopeptidases

Basic information

Region (hg38): 18:74534499-74587212

Links

ENSG00000150656 ∙ NCBI:84735 ∙ OMIM:609064 ∙ HGNC:20675 ∙ Uniprot:Q96KN2 ∙ 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 CNDP1 gene.

• Inborn genetic diseases (26 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNDP1 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			25	1	5	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	25	2	5

Variants in CNDP1

This is a list of pathogenic ClinVar variants found in the CNDP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-74556342-C-T		not specified	Uncertain significance (Nov 09, 2023)
18-74556352-G-GGCTGT		CNDP1-related disorder	Likely benign (Feb 17, 2023)
18-74556378-G-A		not specified	Uncertain significance (Oct 03, 2022)
18-74556402-C-T		not specified	Likely benign (May 16, 2023)
18-74556411-C-A		not specified	Uncertain significance (Nov 18, 2022)
18-74556411-C-T		not specified	Uncertain significance (Jul 08, 2022)
18-74559353-G-A		not specified	Uncertain significance (Oct 12, 2022)
18-74559375-G-A		not specified	Uncertain significance (Feb 14, 2023)
18-74559395-A-G		not specified	Uncertain significance (Jan 24, 2023)
18-74559407-G-A		not specified	Uncertain significance (Feb 21, 2024)
18-74559437-G-T		not specified	Uncertain significance (Jul 09, 2021)
18-74560862-G-A		not specified	Uncertain significance (May 27, 2022)
18-74560920-C-T		not specified	Uncertain significance (Mar 29, 2023)
18-74560929-C-T		not specified	Uncertain significance (Nov 21, 2023)
18-74560970-C-T		not specified	Uncertain significance (Aug 17, 2021)
18-74560993-C-A		not specified	Uncertain significance (Mar 06, 2023)
18-74560998-A-G		not specified	Uncertain significance (Apr 13, 2023)
18-74562062-G-C		not specified	Uncertain significance (Jun 13, 2023)
18-74567350-G-A		not specified	Uncertain significance (Dec 15, 2021)
18-74567371-A-T		not specified	Uncertain significance (Jul 19, 2023)
18-74567390-C-T			Benign (Dec 31, 2019)
18-74567408-G-A		not specified	Uncertain significance (Jun 16, 2023)
18-74571177-ACT-A			Benign (Dec 31, 2019)
18-74576913-T-A		not specified	Uncertain significance (Oct 26, 2021)
18-74576965-T-C		not specified	Uncertain significance (Feb 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNDP1	protein_coding	protein_coding	ENST00000358821	12	52774

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.18e-9	0.779	125259	0	489	125748	0.00195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.418	291	312	0.933	0.0000186	3305
Missense in Polyphen		108	108.33	0.99699		1215
Synonymous	-0.405	133	127	1.05	0.00000857	1010
Loss of Function	1.55	18	26.6	0.676	0.00000150	282

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00275	0.00272
Ashkenazi Jewish	0.000215	0.000198
East Asian	0.00288	0.00289
Finnish	0.000729	0.000693
European (Non-Finnish)	0.00319	0.00307
Middle Eastern	0.00288	0.00289
South Asian	0.000163	0.000163
Other	0.00204	0.00196

dbNSFP

Source: dbNSFP

• Pathway: Arginine and proline metabolism - Homo sapiens (human);beta-Alanine metabolism - Homo sapiens (human);Histidine metabolism - Homo sapiens (human);Carnosinuria, carnosinemia;Ureidopropionase deficiency;GABA-Transaminase Deficiency;Histidine Metabolism;Beta-Alanine Metabolism;Histidinemia;DroToll-like;Histidine metabolism;Histidine degradation (Consensus)

Recessive Scores

• pRec: 0.242

Intolerance Scores

• loftool: 0.932
• rvis_EVS: 1.25
• rvis_percentile_EVS: 93.44

Haploinsufficiency Scores

• pHI: 0.120
• hipred: N
• hipred_score: 0.228
• ghis: 0.396

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.223

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cndp1

Gene ontology

• Biological process: proteolysis;regulation of cellular protein metabolic process
• Cellular component: extracellular region;cytosol
• Molecular function: carboxypeptidase activity;metallopeptidase activity;dipeptidase activity;metal ion binding