KNOP1

lysine rich nucleolar protein 1

Basic information

Region (hg38): 16:19701937-19718235

Previous symbols: [ "C16orf88" ]

Links

ENSG00000103550NCBI:400506HGNC:34404Uniprot:Q1ED39AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
5
clinvar
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
16-19706998-C-T not specified Uncertain significance (Oct 16, 2023)3116132
16-19706999-G-A not specified Uncertain significance (Mar 01, 2024)2403260
16-19707010-C-A not specified Uncertain significance (May 25, 2022)2290819
16-19707022-C-T not specified Uncertain significance (Jul 06, 2022)2282324
16-19707088-G-A not specified Uncertain significance (Mar 19, 2024)3289218
16-19707113-G-A not specified Uncertain significance (Jul 14, 2023)2598400
16-19707140-A-G not specified Uncertain significance (Sep 16, 2021)3116131
16-19707173-G-C not specified Uncertain significance (Jun 02, 2023)2519563
16-19711398-T-C not specified Uncertain significance (Dec 27, 2023)3116138
16-19711410-C-T not specified Uncertain significance (Jan 22, 2024)3116137
16-19714158-T-C not specified Uncertain significance (Nov 17, 2022)2208293
16-19714192-C-T not specified Uncertain significance (Nov 21, 2023)3116136
16-19714278-G-A not specified Likely benign (Aug 02, 2022)2357579
16-19714333-T-C not specified Uncertain significance (Dec 14, 2022)2398221
16-19714401-A-C not specified Uncertain significance (Sep 27, 2021)2252353
16-19714410-T-C not specified Likely benign (Nov 08, 2022)2394099
16-19714437-C-T not specified Uncertain significance (Feb 01, 2023)2456821
16-19714469-C-A not specified Uncertain significance (Jan 10, 2022)3116134
16-19714519-C-T not specified Uncertain significance (Jan 23, 2023)2462204
16-19714575-T-C not specified Uncertain significance (Jan 23, 2023)2456256
16-19714593-A-G not specified Uncertain significance (Nov 29, 2023)3116133
16-19714612-T-G not specified Uncertain significance (Nov 22, 2021)2262138
16-19714633-G-C not specified Uncertain significance (Mar 29, 2022)2280173
16-19714756-C-G not specified Uncertain significance (Mar 31, 2024)3289217
16-19714776-G-A not specified Likely benign (Feb 27, 2023)2454944

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
KNOP1protein_codingprotein_codingENST00000219837 414656
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.39e-70.4901251800521252320.000208
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.1282522580.9780.00001423028
Missense in Polyphen5463.1670.85488865
Synonymous0.01241011010.9980.00000609853
Loss of Function0.8451215.60.7698.06e-7217

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003520.000350
Ashkenazi Jewish0.000.00
East Asian0.0003320.000326
Finnish0.0007430.000739
European (Non-Finnish)0.0001610.000159
Middle Eastern0.0003320.000326
South Asian0.0001970.000196
Other0.000.00

dbNSFP

Source: dbNSFP

Intolerance Scores

loftool
rvis_EVS
0.04
rvis_percentile_EVS
57.41

Haploinsufficiency Scores

pHI
hipred
N
hipred_score
0.123
ghis
0.530

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
gene_indispensability_score

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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

Biological process
Cellular component
nucleolus
Molecular function
RNA binding