CNDP2
Basic information
Region (hg38): 18:74495816-74523454
Previous symbols: [ "PEPA" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNDP2 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 | 2 | |||||
missense | 38 | 41 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 1 | 1 | ||||
non coding | 1 | |||||
Total | 0 | 0 | 38 | 5 | 1 |
Variants in CNDP2
This is a list of pathogenic ClinVar variants found in the CNDP2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
18-74499978-C-T | not specified | Uncertain significance (Jul 09, 2021) | ||
18-74500006-A-G | not specified | Uncertain significance (May 11, 2022) | ||
18-74500019-G-A | not specified | Uncertain significance (Jul 31, 2024) | ||
18-74501350-A-G | not specified | Uncertain significance (Aug 27, 2024) | ||
18-74501359-G-A | not specified | Uncertain significance (Dec 09, 2023) | ||
18-74501366-C-T | not specified | Uncertain significance (Nov 13, 2024) | ||
18-74501372-C-T | Benign (Jul 03, 2018) | |||
18-74505871-C-T | not specified | Uncertain significance (Oct 05, 2023) | ||
18-74505882-A-G | not specified | Uncertain significance (Oct 21, 2024) | ||
18-74505895-G-T | not specified | Uncertain significance (Jan 03, 2024) | ||
18-74505924-G-A | not specified | Uncertain significance (Jan 31, 2022) | ||
18-74505930-A-G | not specified | Uncertain significance (Jul 28, 2021) | ||
18-74505945-G-A | not specified | Uncertain significance (Aug 02, 2024) | ||
18-74505979-A-G | not specified | Uncertain significance (Sep 01, 2021) | ||
18-74505987-C-G | not specified | Uncertain significance (Feb 05, 2024) | ||
18-74506020-C-T | Likely benign (Jun 26, 2018) | |||
18-74508879-C-T | not specified | Uncertain significance (May 11, 2022) | ||
18-74508886-C-T | Likely benign (Dec 01, 2017) | |||
18-74508887-G-A | not specified | Uncertain significance (Sep 06, 2022) | ||
18-74508902-C-A | not specified | Uncertain significance (Oct 25, 2023) | ||
18-74508924-G-T | not specified | Uncertain significance (Nov 21, 2022) | ||
18-74510816-A-T | not specified | Uncertain significance (Aug 08, 2023) | ||
18-74510819-C-T | not specified | Uncertain significance (Mar 01, 2024) | ||
18-74510842-C-T | Likely benign (Jul 03, 2018) | |||
18-74510876-G-A | not specified | Uncertain significance (Nov 08, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
CNDP2 | protein_coding | protein_coding | ENST00000324262 | 11 | 25316 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.01e-7 | 0.930 | 125695 | 0 | 53 | 125748 | 0.000211 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.110 | 289 | 294 | 0.982 | 0.0000179 | 3116 |
Missense in Polyphen | 67 | 89.671 | 0.74718 | 954 | ||
Synonymous | -0.345 | 142 | 137 | 1.04 | 0.0000104 | 928 |
Loss of Function | 1.82 | 15 | 24.8 | 0.605 | 0.00000130 | 268 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000398 | 0.000398 |
Ashkenazi Jewish | 0.000298 | 0.000298 |
East Asian | 0.000109 | 0.000109 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000257 | 0.000255 |
Middle Eastern | 0.000109 | 0.000109 |
South Asian | 0.000229 | 0.000229 |
Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Hydrolyzes a variety of dipeptides including L-carnosine but has a strong preference for Cys-Gly (PubMed:19346245). Acts as a functional tumor suppressor in gastric cancer via activation of the mitogen-activated protein kinase (MAPK) pathway. An elevated level of CNDP2 activates the p38 and JNK MAPK pathways to induce cell apoptosis, and a lower level of CNDP2 activates the ERK MAPK pathway to promote cell proliferation (PubMed:24395568). Isoform 2 may play a role as tumor suppressor in hepatocellular carcinoma (HCC) cells (PubMed:17121880). Catalyzes the production of N- lactoyl-amino acids from lactate and amino acids by reverse proteolysis (PubMed:25964343). {ECO:0000269|PubMed:17121880, ECO:0000269|PubMed:19346245, ECO:0000269|PubMed:24395568, ECO:0000269|PubMed:25964343}.;
- Pathway
- Arginine and proline metabolism - Homo sapiens (human);beta-Alanine metabolism - Homo sapiens (human);Histidine metabolism - Homo sapiens (human);Glutathione conjugation;Phase II - Conjugation of compounds;Biological oxidations;Metabolism;γ-glutamyl cycle;Glutathione synthesis and recycling
(Consensus)
Recessive Scores
- pRec
- 0.418
Intolerance Scores
- loftool
- 0.396
- rvis_EVS
- -0.75
- rvis_percentile_EVS
- 13.67
Haploinsufficiency Scores
- pHI
- 0.274
- hipred
- N
- hipred_score
- 0.426
- ghis
- 0.544
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.373
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cndp2
- Phenotype
Gene ontology
- Biological process
- proteolysis;glutathione biosynthetic process
- Cellular component
- nucleoplasm;cytosol;extracellular exosome
- Molecular function
- carboxypeptidase activity;metallopeptidase activity;metal ion binding;cytosolic dipeptidase activity;alanylglutamate dipeptidase activity