CRNKL1
Basic information
Region (hg38): 20:20034368-20056046
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 33 | ||||
nonsense | 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) | ||
20-20036212-C-T | not specified | Uncertain significance (Dec 19, 2023) | ||
20-20036229-T-C | not specified | Uncertain significance (Dec 15, 2022) | ||
20-20036362-A-T | not specified | Uncertain significance (Aug 26, 2022) | ||
20-20037426-C-T | not specified | Uncertain significance (Mar 16, 2022) | ||
20-20037528-T-C | not specified | Uncertain significance (Jan 31, 2023) | ||
20-20037566-C-G | not specified | Uncertain significance (Feb 13, 2024) | ||
20-20038365-C-T | not specified | Uncertain significance (Nov 28, 2023) | ||
20-20038392-C-T | not specified | Uncertain significance (Sep 12, 2023) | ||
20-20039650-A-T | not specified | Uncertain significance (Aug 12, 2022) | ||
20-20039670-A-G | not specified | Uncertain significance (Mar 07, 2024) | ||
20-20039722-T-A | not specified | Uncertain significance (Jan 24, 2023) | ||
20-20039761-G-C | not specified | Uncertain significance (Jan 16, 2024) | ||
20-20039839-T-C | not specified | Uncertain significance (Dec 27, 2023) | ||
20-20040750-A-G | not specified | Uncertain significance (Jul 27, 2023) | ||
20-20040759-A-C | not specified | Uncertain significance (May 22, 2023) | ||
20-20041625-C-A | not specified | Uncertain significance (Apr 23, 2024) | ||
20-20042353-T-A | not specified | Uncertain significance (Jan 23, 2023) | ||
20-20042411-C-G | not specified | Uncertain significance (Oct 27, 2022) | ||
20-20042459-C-T | not specified | Uncertain significance (Feb 06, 2023) | ||
20-20042476-C-T | not specified | Uncertain significance (May 17, 2023) | ||
20-20042492-A-G | not specified | Uncertain significance (Dec 14, 2023) | ||
20-20043543-A-C | not specified | Uncertain significance (Jan 03, 2024) | ||
20-20043629-G-C | not specified | Uncertain significance (Jun 04, 2024) | ||
20-20045441-C-T | not specified | Uncertain significance (Oct 22, 2021) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
CRNKL1 | protein_coding | protein_coding | ENST00000377340 | 15 | 21679 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00000272 | 1.00 | 125613 | 0 | 135 | 125748 | 0.000537 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.880 | 420 | 474 | 0.886 | 0.0000259 | 5565 |
Missense in Polyphen | 57 | 107.1 | 0.53221 | 1178 | ||
Synonymous | -0.805 | 187 | 174 | 1.08 | 0.00000932 | 1546 |
Loss of Function | 4.16 | 19 | 51.1 | 0.372 | 0.00000293 | 565 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00656 | 0.00646 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000194 | 0.000193 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000327 | 0.0000327 |
Other | 0.000495 | 0.000489 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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