HNRNPL
Basic information
Region (hg38): 19:38836370-38852347
Previous symbols: [ "HNRPL" ]
Links
Phenotypes
GenCC
Source:
- complex neurodevelopmental disorder (Limited), mode of inheritance: AR
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (49 variants)
- not_provided (6 variants)
- Neuromuscular_disease (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the HNRNPL gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001533.3. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | |||||
| missense | 49 | 49 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 50 | 1 | 3 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HNRNPL | protein_coding | protein_coding | ENST00000221419 | 13 | 15960 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.997 | 0.00315 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.54 | 144 | 323 | 0.446 | 0.0000184 | 3809 |
| Missense in Polyphen | 25 | 96.315 | 0.25957 | 1179 | ||
| Synonymous | -4.72 | 197 | 129 | 1.53 | 0.00000822 | 1137 |
| Loss of Function | 4.34 | 2 | 25.8 | 0.0776 | 0.00000118 | 322 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Splicing factor binding to exonic or intronic sites and acting as either an activator or repressor of exon inclusion. Exhibits a binding preference for CA-rich elements (PubMed:11809897, PubMed:22570490, PubMed:24164894, PubMed:25623890, PubMed:26051023). Component of the heterogeneous nuclear ribonucleoprotein (hnRNP) complexes and associated with most nascent transcripts (PubMed:2687284). Associates, together with APEX1, to the negative calcium responsive element (nCaRE) B2 of the APEX2 promoter (PubMed:11809897). {ECO:0000269|PubMed:11809897, ECO:0000269|PubMed:22570490, ECO:0000269|PubMed:25623890, ECO:0000269|PubMed:26051023, ECO:0000269|PubMed:2687284}.;
- Pathway
- mRNA Processing;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Intolerance Scores
- loftool
- rvis_EVS
- -0.63
- rvis_percentile_EVS
- 17.03
Haploinsufficiency Scores
- pHI
- 0.893
- hipred
- Y
- hipred_score
- 0.818
- ghis
- 0.613
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.995
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hnrnpl
- Phenotype
- immune system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- regulation of alternative mRNA splicing, via spliceosome;mRNA splicing, via spliceosome;RNA processing;circadian rhythm;RNA metabolic process;cellular response to amino acid starvation;positive regulation of translation;negative regulation of mRNA splicing, via spliceosome;response to peptide;positive regulation of mRNA binding
- Cellular component
- nucleus;nucleoplasm;cytosol;membrane;ribonucleoprotein granule;pronucleus;perinuclear region of cytoplasm;extracellular exosome;ribonucleoprotein complex
- Molecular function
- RNA binding;mRNA 3'-UTR binding;protein binding;transcription regulatory region DNA binding;pre-mRNA intronic binding;mRNA CDS binding