KNOP1

lysine rich nucleolar protein 1

Basic information

Region (hg38): 16:19701937-19718235

Previous symbols: [ "C16orf88" ]

Links

ENSG00000103550 ∙ NCBI:400506 ∙ ∙ HGNC:34404 ∙ Uniprot:Q1ED39 ∙ 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 KNOP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KNOP1 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			21	5		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	5	0

Variants in KNOP1

This is a list of pathogenic ClinVar variants found in the KNOP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-19706962-T-C		not specified	Uncertain significance (Jul 17, 2024)
16-19706998-C-T		not specified	Uncertain significance (Oct 16, 2023)
16-19706999-G-A		not specified	Uncertain significance (Mar 01, 2024)
16-19707010-C-A		not specified	Uncertain significance (May 25, 2022)
16-19707022-C-T		not specified	Uncertain significance (Nov 13, 2024)
16-19707088-G-A		not specified	Uncertain significance (Mar 19, 2024)
16-19707113-G-A		not specified	Uncertain significance (Jul 14, 2023)
16-19707140-A-G		not specified	Uncertain significance (Sep 16, 2021)
16-19707173-G-C		not specified	Uncertain significance (Jun 02, 2023)
16-19711398-T-C		not specified	Uncertain significance (Dec 27, 2023)
16-19711410-C-T		not specified	Uncertain significance (Jan 22, 2024)
16-19711430-G-A		not specified	Uncertain significance (Sep 24, 2024)
16-19714131-T-C		not specified	Uncertain significance (Jun 26, 2024)
16-19714158-T-C		not specified	Uncertain significance (Nov 17, 2022)
16-19714173-C-T		not specified	Uncertain significance (Aug 01, 2024)
16-19714192-C-T		not specified	Uncertain significance (Nov 21, 2023)
16-19714278-G-A		not specified	Likely benign (Aug 02, 2022)
16-19714333-T-C		not specified	Uncertain significance (Dec 14, 2022)
16-19714401-A-C		not specified	Uncertain significance (Sep 27, 2021)
16-19714410-T-C		not specified	Likely benign (Nov 08, 2022)
16-19714437-C-T		not specified	Uncertain significance (Feb 01, 2023)
16-19714469-C-A		not specified	Uncertain significance (Jan 10, 2022)
16-19714519-C-T		not specified	Uncertain significance (Jan 23, 2023)
16-19714542-G-A		not specified	Uncertain significance (Nov 15, 2024)
16-19714575-T-C		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KNOP1	protein_coding	protein_coding	ENST00000219837	4	14656

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.39e-7	0.490	125180	0	52	125232	0.000208

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.128	252	258	0.978	0.0000142	3028
Missense in Polyphen		54	63.167	0.85488		865
Synonymous	0.0124	101	101	0.998	0.00000609	853
Loss of Function	0.845	12	15.6	0.769	8.06e-7	217

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000352	0.000350
Ashkenazi Jewish	0.00	0.00
East Asian	0.000332	0.000326
Finnish	0.000743	0.000739
European (Non-Finnish)	0.000161	0.000159
Middle Eastern	0.000332	0.000326
South Asian	0.000197	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.41

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123
• ghis: 0.530

Essentials

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

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Knop1
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype

Gene ontology

• Cellular component: nucleolus
• Molecular function: RNA binding