NOPCHAP1

NOP protein chaperone 1

Basic information

Region (hg38): 12:104986316-105074197

Previous symbols: [ "C12orf45" ]

Links

ENSG00000151131 ∙ NCBI:121053 ∙ ∙ HGNC:28628 ∙ Uniprot:Q8N5I9 ∙ 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 NOPCHAP1 gene.

• Inborn genetic diseases (24 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NOPCHAP1 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			21	3		24
Total	0	0	21	3	0

Variants in NOPCHAP1

This is a list of pathogenic ClinVar variants found in the NOPCHAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-105024435-G-C		not specified	Uncertain significance (Mar 03, 2022)
12-105026736-T-G		not specified	Uncertain significance (May 17, 2023)
12-105030409-C-T		not specified	Uncertain significance (Nov 18, 2022)
12-105031790-C-T		not specified	Uncertain significance (Jan 23, 2024)
12-105034301-A-G		not specified	Uncertain significance (Jul 14, 2021)
12-105034346-C-T		not specified	Uncertain significance (Dec 01, 2023)
12-105034376-T-G		not specified	Uncertain significance (Jul 08, 2022)
12-105038129-A-G		not specified	Uncertain significance (Feb 12, 2024)
12-105038141-T-C		not specified	Uncertain significance (Sep 14, 2021)
12-105038171-G-A		not specified	Uncertain significance (Dec 28, 2022)
12-105039776-T-G		not specified	Uncertain significance (Nov 06, 2023)
12-105040631-C-A		not specified	Uncertain significance (Apr 28, 2023)
12-105040690-G-A		not specified	Uncertain significance (Nov 17, 2023)
12-105046933-G-T		not specified	Uncertain significance (Feb 28, 2024)
12-105049919-C-T		not specified	Uncertain significance (Jun 09, 2022)
12-105049956-C-T		not specified	Uncertain significance (Jun 26, 2023)
12-105049980-C-G		not specified	Uncertain significance (Mar 07, 2023)
12-105050053-G-A		not specified	Uncertain significance (Feb 21, 2024)
12-105052205-C-T		not specified	Uncertain significance (Sep 23, 2023)
12-105052835-T-A		not specified	Uncertain significance (Aug 01, 2022)
12-105058140-C-T		not specified	Likely benign (Mar 21, 2023)
12-105061748-G-A		not specified	Likely benign (Apr 06, 2023)
12-105062890-C-G		not specified	Uncertain significance (Feb 12, 2024)
12-105062929-T-C		not specified	Uncertain significance (Jan 30, 2024)
12-105062932-C-T		not specified	Uncertain significance (Nov 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOPCHAP1	protein_coding	protein_coding	ENST00000552951	4	63428

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0105	0.842	124774	0	14	124788	0.0000561

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00821	98	98.2	0.998	0.00000488	1208
Missense in Polyphen		19	22.478	0.84525		338
Synonymous	0.0949	33	33.7	0.979	0.00000158	344
Loss of Function	1.17	4	7.45	0.537	3.16e-7	98

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000156	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000557	0.0000556
Finnish	0.0000515	0.0000464
European (Non-Finnish)	0.0000717	0.0000618
Middle Eastern	0.0000557	0.0000556
South Asian	0.0000337	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0889

Intolerance Scores

• loftool: 0.599
• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.27

Haploinsufficiency Scores

• pHI: 0.166
• hipred: N
• hipred_score: 0.172
• ghis: 0.548

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: D10Wsu102e