NOC4L

nucleolar complex associated 4 homolog, the group of Armadillo like helical domain containing|SSU processome

Basic information

Region (hg38): 12:132144457-132152473

Links

ENSG00000184967 ∙ NCBI:79050 ∙ OMIM:612819 ∙ HGNC:28461 ∙ Uniprot:Q9BVI4 ∙ 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 NOC4L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NOC4L 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		2
missense			86	3		89
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	86	5	0

Variants in NOC4L

This is a list of pathogenic ClinVar variants found in the NOC4L region.

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

Position	Type	Phenotype	Significance	ClinVar
12-132144495-C-T		not specified	Uncertain significance (May 31, 2023)
12-132144508-C-T		not specified	Uncertain significance (Mar 31, 2022)
12-132144523-G-C		not specified	Uncertain significance (Nov 14, 2024)
12-132144526-C-G		not specified	Uncertain significance (Jun 18, 2021)
12-132144534-C-G		not specified	Uncertain significance (Oct 12, 2021)
12-132144540-C-A		not specified	Uncertain significance (Oct 28, 2024)
12-132144908-G-A		not specified	Uncertain significance (May 13, 2024)
12-132144959-G-C		not specified	Uncertain significance (Mar 31, 2024)
12-132145604-G-A		not specified	Uncertain significance (Dec 21, 2023)
12-132145613-G-A		not specified	Uncertain significance (Oct 05, 2023)
12-132145621-A-C		not specified	Uncertain significance (Mar 06, 2023)
12-132147307-G-C		not specified	Uncertain significance (Jun 05, 2023)
12-132147345-C-T		not specified	Uncertain significance (Feb 20, 2025)
12-132147636-G-T		not specified	Uncertain significance (Feb 08, 2025)
12-132147642-G-C		not specified	Uncertain significance (Nov 26, 2024)
12-132147681-C-G		not specified	Uncertain significance (Jun 24, 2022)
12-132147694-G-C		not specified	Uncertain significance (Jan 30, 2024)
12-132147713-C-G		not specified	Uncertain significance (Nov 17, 2022)
12-132147747-G-A		not specified	Uncertain significance (Oct 18, 2021)
12-132147759-C-T		not specified	Uncertain significance (Jul 02, 2024)
12-132147889-G-A		not specified	Likely benign (May 13, 2024)
12-132147897-G-T		not specified	Uncertain significance (Dec 27, 2023)
12-132147924-C-T			Likely benign (Apr 01, 2025)
12-132147929-G-A		not specified	Uncertain significance (Oct 26, 2021)
12-132147937-C-T		not specified	Uncertain significance (Mar 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOC4L	protein_coding	protein_coding	ENST00000330579	15	8021

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00108	0.999	125412	3	72	125487	0.000299

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.47	448	323	1.39	0.0000218	3256
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000301	0.0000301
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000777	0.0000618
Middle Eastern	0.0000545	0.0000544
South Asian	0.00214	0.00209
Other	0.000542	0.000327

dbNSFP

Source: dbNSFP

• Pathway: rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.315
• rvis_EVS: -1.28
• rvis_percentile_EVS: 5.17

Haploinsufficiency Scores

• pHI: 0.543
• ghis: 0.574

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.980

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Noc4l

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;rRNA processing
• Cellular component: nucleus;nucleoplasm;nucleolus;integral component of membrane;Noc4p-Nop14p complex;nuclear membrane;small-subunit processome
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;RNA binding;protein binding