NOC4L

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				5 clinvar		5
missense			152 clinvar	7 clinvar		159
nonsense						0
start loss						0
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	0	160	13	0	173

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 49 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024078.3	RefSeq	NP_076983.1	15	MANE Select
ENST00000330579.6	Ensembl	ENSP00000328854.1	15	MANE Select
NM_001414688.1	RefSeq	NP_001401617.1	14	Standard
NM_001414689.1	RefSeq	NP_001401618.1	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

rRNA processing
Metabolism of RNA
rRNA modification in the nucleus and cytosol
rRNA processing in the nucleus and cytosol

Biological Process

regulation of transcription by RNA polymerase II
rRNA processing

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
RNA binding
protein binding

Cellular Component

nucleus
nucleoplasm
nucleolus
integral component of membrane
Noc4p-Nop14p complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000330579
Coding exons: 15
Length: 8021
Individuals with no LoFs: 125412
Homozygous LoFs: 3
Heterozygous LoFs: 72
Defined: 125487
p: 0.000299

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-2.47	448	323	1.39	0.0000218	3256
Missense (PolyPhen)		135	93.471	1.4443		1032
Synonymous	-5.24	219	140	1.56	0.00000933	1057
Loss of Function	3.08	10	27.4	0.365	0.00000135	304

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000030	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000078	0.000062	rare
South Asian	0.0021	0.0021	notable
Other	0.00054	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.315
RVIS EVS: -1.28
RVIS percentile EVS: 5.17

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.980

Gene Damage Prediction

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