CNPPD1

cyclin Pas1/PHO80 domain containing 1

Basic information

Region (hg38): 2:219171897-219178106

Previous symbols: [ "C2orf24" ]

Links

ENSG00000115649 ∙ NCBI:27013 ∙ ∙ HGNC:25220 ∙ Uniprot:Q9BV87 ∙ 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 CNPPD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNPPD1 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			30			30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	0	0

Variants in CNPPD1

This is a list of pathogenic ClinVar variants found in the CNPPD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-219172614-C-T		not specified	Uncertain significance (Jun 10, 2024)
2-219172663-G-A		not specified	Uncertain significance (Apr 07, 2023)
2-219172695-G-T		not specified	Uncertain significance (Feb 14, 2023)
2-219172701-A-T		not specified	Uncertain significance (Aug 28, 2023)
2-219172707-T-C		not specified	Uncertain significance (Oct 26, 2022)
2-219172744-C-T		not specified	Uncertain significance (Mar 28, 2024)
2-219172757-G-C		not specified	Uncertain significance (Feb 07, 2023)
2-219172770-T-C		not specified	Likely benign (May 15, 2024)
2-219172828-T-C		not specified	Uncertain significance (Sep 16, 2022)
2-219172872-A-T		not specified	Uncertain significance (Mar 15, 2024)
2-219172912-T-A		not specified	Uncertain significance (Aug 02, 2023)
2-219172935-A-T		not specified	Uncertain significance (May 13, 2024)
2-219172953-A-G		not specified	Uncertain significance (May 13, 2022)
2-219173019-G-A		not specified	Uncertain significance (Oct 06, 2022)
2-219173082-G-A		not specified	Uncertain significance (Sep 26, 2022)
2-219173112-G-A		not specified	Uncertain significance (Dec 21, 2023)
2-219173396-G-A		not specified	Uncertain significance (Dec 14, 2021)
2-219173423-G-A		not specified	Uncertain significance (Jul 09, 2021)
2-219173448-G-A		not specified	Uncertain significance (Aug 28, 2023)
2-219174168-C-T		not specified	Uncertain significance (Feb 06, 2024)
2-219174183-G-A		not specified	Uncertain significance (Jan 26, 2022)
2-219174810-T-C		not specified	Uncertain significance (Jun 29, 2023)
2-219174825-C-T		not specified	Uncertain significance (Apr 12, 2023)
2-219174839-G-A		not specified	Uncertain significance (Oct 12, 2022)
2-219174876-C-T		not specified	Uncertain significance (Dec 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNPPD1	protein_coding	protein_coding	ENST00000409789	8	6210

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.64e-9	0.707	125681	0	67	125748	0.000266

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.145	233	239	0.974	0.0000134	2596
Missense in Polyphen		71	62.81	1.1304		721
Synonymous	-0.0577	101	100	1.01	0.00000543	878
Loss of Function	1.36	16	23.1	0.694	0.00000125	222

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000391	0.000391
Ashkenazi Jewish	0.00	0.00
East Asian	0.00163	0.00163
Finnish	0.00	0.00
European (Non-Finnish)	0.000177	0.000176
Middle Eastern	0.00163	0.00163
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 1.15
• rvis_percentile_EVS: 92.56

Haploinsufficiency Scores

• pHI: 0.227
• hipred: N
• hipred_score: 0.167
• ghis: 0.378

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	High	Medium	High
Cancer	High	Medium	High

Mouse Genome Informatics

• Gene name: Cnppd1

Gene ontology

• Biological process: regulation of cyclin-dependent protein serine/threonine kinase activity
• Cellular component: integral component of membrane
• Molecular function: protein kinase binding