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): 20:20034367-20056046

Links

ENSG00000101343 ∙ NCBI:51340 ∙ OMIM:610952 ∙ HGNC:15762 ∙ Uniprot:Q9BZJ0 ∙ 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 CRNKL1 gene.

• Inborn genetic diseases (22 variants)
• not provided (1 variants)

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			22			22
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	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)
20-20042353-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 (Feb 10, 2022)
20-20045441-C-T		not specified	Uncertain significance (Oct 22, 2021)
20-20047786-C-A		not specified	Uncertain significance (Apr 07, 2022)

GnomAD

Source: gnomAD

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: 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

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

Mouse Genome Informatics

• Gene name: Crnkl1

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