CRNKL1

crooked neck pre-mRNA splicing factor 1, the group of Spliceosomal C complex|Spliceosomal B complex|Spliceosomal Bact complex|Spliceosomal P complex

Basic information

Region (hg38): 20:20034368-20056046

Links

ENSG00000101343NCBI:51340OMIM:610952HGNC:15762Uniprot:Q9BZJ0AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CRNKL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRNKL1 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
33
clinvar
33
nonsense
1
clinvar
1
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 33 1 0

Variants in CRNKL1

This is a list of pathogenic ClinVar variants found in the CRNKL1 region.

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

Position Type Phenotype Significance ClinVar
20-20036211-T-G not specified Uncertain significance (Mar 20, 2023)2521687
20-20036212-C-T not specified Uncertain significance (Dec 19, 2023)3077558
20-20036229-T-C not specified Uncertain significance (Dec 15, 2022)2335916
20-20036362-A-T not specified Uncertain significance (Aug 26, 2022)2376289
20-20037426-C-T not specified Uncertain significance (Mar 16, 2022)2207868
20-20037528-T-C not specified Uncertain significance (Jan 31, 2023)2480059
20-20037566-C-G not specified Uncertain significance (Feb 13, 2024)3077557
20-20038365-C-T not specified Uncertain significance (Nov 28, 2023)3077556
20-20038392-C-T not specified Uncertain significance (Sep 12, 2023)2598298
20-20039650-A-T not specified Uncertain significance (Aug 12, 2022)2306737
20-20039670-A-G not specified Uncertain significance (Mar 07, 2024)3077555
20-20039722-T-A not specified Uncertain significance (Jan 24, 2023)2473326
20-20039761-G-C not specified Uncertain significance (Jan 16, 2024)3077554
20-20039839-T-C not specified Uncertain significance (Dec 27, 2023)3077553
20-20040750-A-G not specified Uncertain significance (Jul 27, 2023)2609309
20-20040759-A-C not specified Uncertain significance (May 22, 2023)2549495
20-20041625-C-A not specified Uncertain significance (Apr 23, 2024)3269565
20-20042353-T-A not specified Uncertain significance (Jan 23, 2023)2477370
20-20042411-C-G not specified Uncertain significance (Oct 27, 2022)2222786
20-20042459-C-T not specified Uncertain significance (Feb 06, 2023)3077552
20-20042476-C-T not specified Uncertain significance (May 17, 2023)2548243
20-20042492-A-G not specified Uncertain significance (Dec 14, 2023)3077551
20-20043543-A-C not specified Uncertain significance (Jan 03, 2024)3077550
20-20043629-G-C not specified Uncertain significance (Jun 04, 2024)2407528
20-20045441-C-T not specified Uncertain significance (Oct 22, 2021)2256747

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CRNKL1protein_codingprotein_codingENST00000377340 1521679
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.000002721.0012561301351257480.000537
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.8804204740.8860.00002595565
Missense in Polyphen57107.10.532211178
Synonymous-0.8051871741.080.000009321546
Loss of Function4.161951.10.3720.00000293565

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.006560.00646
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.0001940.000193
Middle Eastern0.000.00
South Asian0.00003270.0000327
Other0.0004950.000489

dbNSFP

Source: dbNSFP

Function
FUNCTION: Involved in pre-mRNA splicing process. {ECO:0000269|PubMed:11991638, ECO:0000269|PubMed:12084575, ECO:0000269|PubMed:28076346, ECO:0000269|PubMed:28502770}.;
Pathway
Spliceosome - Homo sapiens (human);Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

pRec
0.175

Intolerance Scores

loftool
0.509
rvis_EVS
1.05
rvis_percentile_EVS
91.35

Haploinsufficiency Scores

pHI
0.292
hipred
N
hipred_score
0.398
ghis
0.551

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
N
gene_indispensability_score
0.0941

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Crnkl1
Phenotype

Gene ontology

Biological process
spliceosomal complex assembly;mRNA splicing, via spliceosome
Cellular component
Prp19 complex;nucleus;nucleoplasm;spliceosomal complex;nuclear speck;U2-type catalytic step 2 spliceosome;catalytic step 2 spliceosome;post-mRNA release spliceosomal complex
Molecular function
RNA binding;protein binding