NOPCHAP1

protein-coding

NOP protein chaperone 1

Gene summary

Enables box C/D methylation guide snoRNP complex binding activity. Involved in box C/D snoRNP assembly. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C12orf45

MANE transcript

NM_152318.3

Inheritance

—

ClinVar variants

U:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr12:104,986,316-105,074,197

External References & Databases

Ensembl (ENSG00000151131)

Transcript & Mutation Effects

hg38 • Region Span ~87.9 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 NOPCHAP1 variants in ClinVar

0 Conditions Cataloged

No annotated ClinVar phenotypes.

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152318.3. 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
missense			2 clinvar			2
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	3	0	0	3

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152318.3	RefSeq	NP_689531.2	4	MANE Select
ENST00000552951.7	Ensembl	ENSP00000447057.1	4	MANE Select
ENST00000280749.5	Ensembl	ENSP00000280749.5	3	Standard
ENST00000280749.6	Ensembl	ENSP00000280749.5	3	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000552951
Coding exons: 4
Length: 63428
Individuals with no LoFs: 124774
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 124788
p: 0.0000561

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.00821	98	98.2	0.998	0.00000488	1208
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000069	0.000065	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000056	0.000056	rare
Finnish	0.000052	0.000046	rare
European (Non-Finnish)	0.000072	0.000062	rare
South Asian	0.000034	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0889

Intolerance Scores

LoFtool: 0.599
RVIS EVS: 0.28
RVIS percentile EVS: 71.27

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): E

Gene Damage Prediction

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