CNDP1

protein-coding

carnosine dipeptidase 1, the group of M20 metallopeptidases

Gene summary

This gene encodes a member of the M20 metalloprotease family. The encoded protein is specifically expressed in the brain, is a homodimeric dipeptidase which was identified as human carnosinase. This gene contains trinucleotide (CTG) repeat length polymorphism in the coding region. [provided by RefSeq, Jul 2008]

MANE transcript

NM_032649.6

Inheritance

—

ClinVar variants

U:73B:19

Top phenotype

CNDP1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.68

Max pathogenic AF

—

Genomic locus

chr18:74,534,500-74,587,212

External References & Databases

Ensembl (ENSG00000150656)

Transcript & Mutation Effects

hg38 • Region Span ~52.7 kb

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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 CNDP1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 85

not providedTotal: 7

CNDP1-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032649.6. 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			72 clinvar	13 clinvar	4 clinvar	89
nonsense						0
start loss						0
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)						0
Total	0	0	73	15	4	92

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032649.6	RefSeq	NP_116038.4	12	MANE Select
ENST00000358821.8	Ensembl	ENSP00000351682.3	12	MANE Select
ENST00000582365.1	Ensembl	ENSP00000462096.1	11	Standard
ENST00000582365.2	Ensembl	ENSP00000462096.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Arginine and proline metabolism - Homo sapiens (human)
beta-Alanine metabolism - Homo sapiens (human)
Histidine metabolism - Homo sapiens (human)
Carnosinuria, carnosinemia
Ureidopropionase deficiency

Biological Process

proteolysis
regulation of cellular protein metabolic process

Molecular Function

carboxypeptidase activity
metallopeptidase activity
dipeptidase activity
metal ion binding

Cellular Component

extracellular region
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000358821
Coding exons: 12
Length: 52774
Individuals with no LoFs: 125259
Homozygous LoFs: 0
Heterozygous LoFs: 489
Defined: 125748
p: 0.00195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.418	291	312	0.933	0.0000186	3305
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0021	0.0021	notable
Latino/Admixed American	0.00062	0.00055	rare
Ashkenazi Jewish	0.00021	0.00020	rare
East Asian	0.0029	0.0029	notable
Finnish	0.00073	0.00069	rare
European (Non-Finnish)	0.0032	0.0031	notable
South Asian	0.00016	0.00016	rare
Other	0.0020	0.0020	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.242

Intolerance Scores

LoFtool: 0.932
RVIS EVS: 1.25
RVIS percentile EVS: 93.44

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.223

Gene Damage Prediction

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