HNRNPK
protein-codingheterogeneous nuclear ribonucleoprotein K, the group of Heterogeneous nuclear ribonucleoproteins|MicroRNA protein coding host genes
Gene summary
This gene belongs to the subfamily of ubiquitously expressed heterogeneous nuclear ribonucleoproteins (hnRNPs). The hnRNPs are RNA binding proteins and they complex with heterogeneous nuclear RNA (hnRNA). These proteins are associated with pre-mRNAs in the nucleus and appear to influence pre-mRNA processing and other aspects of mRNA metabolism and transport. While all of the hnRNPs are present in the nucleus, some seem to shuttle between the nucleus and the cytoplasm. The hnRNP proteins have distinct nucleic acid binding properties. The protein encoded by this gene is located in the nucleoplasm and has three repeats of KH domains that binds to RNAs. It is distinct among other hnRNP proteins in its binding preference; it binds tenaciously to poly(C). This protein is also thought to have a role during cell cycle progession. Several alternatively spliced transcript variants have been described for this gene, however, not all of them are fully characterized. [provided by RefSeq, Jul 2008]
- HNRPK
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~12.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0014700
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0014700
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0018681
Submitter: ClinGen
*HNRNPK* was first reported in relation to autosomal dominant neurodevelopmental disorder-craniofacial dysmorphism-cardiac defect-hip dysplasia syndrome (Au-Kline syndrome) in 2015 (Au et al., PMID: 26173930). Au-Kline syndrome (AKS) is caused by *de novo* variants in *HNRNPK*, leading to variable dysmorphic features, cardiac malformations, developmental delay, and intellectual disability. Multiple patients diagnosed with AKS were initially diagnosed with Kabuki syndrome. Ten variants (all *de novo* loss of function caused by missense, nonsense, frameshift, and splice variants) that have been reported in 10 probands in 5 publications (PMIDs: 26173930, 26954065, 28374925, 28771707, 29904177) are included in this curation. More evidence is available in the literature, but the maximum score for genetic evidence (12 points) has been reached. The mechanism of pathogenicity is known to be loss of function. This gene-disease relationship is also supported by the biochemical function of HNRNPK in osteoclast differentiation as the phenotype involves skeletal abnormalities, including craniosynostosis (PMID: 26638989). In summary, there is definitive evidence to support the relationship between *HNRNPK* and autosomal dominant Au-Kline syndrome. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This gene-disease pair was originally evaluated by the General Gene Curation Expert Panel in 2016. It was reevaluated by the ClinGen Intellectual Disability and Autism Gene Curation Expert Panel on December 21, 2021. As a result of this reevaluation, the classification increased from Moderate to Definitive with the addition of new literature (SOP Version 8).
Inheritance Pattern: AD
Disease ID:MONDO:0014700
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0014700
Submitter: Illumina
The HNRNPK gene is located on chromosome 9 at 9q21.32 and encodes the heterogeneous nuclear ribonucleoprotein K protein, which is one of the major pre-mRNA-binding proteins. HNRNPK was first reported in association with Au Kline syndrome in 2015 (26173930: Au et al. 2015). Evidence supporting this gene-disease relationship includes case-level data and experimental data. At least eight de novo heterozygous variants have been reported in the literature, including fives loss-of-function variants, two missense variants, and one intron variant predicted to result in an inframe insertion, in six publications (26173930: Au et al. 2015; 26954065: Lange et al. 2016; 28771707: Miyake et al. 2017; 28374925: Dentici et al. 2017; 29904177: Au et al. 2018; 32588992: Yamada et al. 2020). The mechanism for disease is loss-of-function. The hnRNP K protein was shown to be expressed in rat hippocampal neuron and colocalized with VGLUT1 (a presynaptic protein) and PSD-95 (a postsynaptic scaffolding protein), and in mouse leukemic monocyte macrophage RAW264.7 cells, a significant increase in GSK3β-hnRNPK interaction was observed (24990929: Folci et al. 2014; 26638989: Fan et al. 2015). In summary, there is strong evidence to support the relationship between HNRNPK and Au Kline syndrome (autosomal dominant).
Inheritance Pattern: AD
Disease ID:MONDO:0014700
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0014700
Submitter: Orphanet
Clinical Genomic Database (CGD)
Manifestation: Cardiovascular; Craniofacial; Musculoskeletal; Neurologic
Intervention: Cardiovascular
Rationale: The condition can involve congenital cardiac anomalies, and awareness may allow early management
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to HNRNPK variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_031263.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 45 | 2 | 49 | ||
| missense | 3 | 30 | 97 | 11 | 1 | 142 |
| nonsense | 4 | 6 | 10 | |||
| start loss | 0 | |||||
| frameshift | 18 | 7 | 1 | 26 | ||
| splice donor/acceptor (+/-2bp) | 9 | 8 | 12 | 29 | ||
| Total | 34 | 51 | 112 | 56 | 3 | 256 |
Highest pathogenic variant AF is 0.0000065725476
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_112553.1 | 15 | MANE Select | |
| Ensembl | ENSP00000365439.3 | 15 | MANE Select | |
| RefSeq | NP_001305115.1 | 14 | Standard | |
| RefSeq | NP_001305116.1 | 14 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- MicroRNAs in cancer - Homo sapiens (human)
- Viral carcinogenesis - Homo sapiens (human)
- Spliceosome - Homo sapiens (human)
- Herpes simplex infection - Homo sapiens (human)
- mRNA Processing
Biological Process
- mRNA splicing, via spliceosome
- RNA processing
- signal transduction
- regulation of low-density lipoprotein particle clearance
- viral process
Molecular Function
- RNA polymerase II proximal promoter sequence-specific DNA binding
- DNA-binding transcription activator activity, RNA polymerase II-specific
- single-stranded DNA binding
- RNA binding
- protein binding
Cellular Component
- nuclear chromatin
- podosome
- nucleus
- nucleoplasm
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000376263
- Coding exons
- 15
- Length
- 12572
- Individuals with no LoFs
- 125435
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 1
- Defined
- 125436
- p
- 0.00000399
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.99 | 93 | 281 | 0.330 | 0.0000162 | 3016 |
| Missense (PolyPhen) | 16 | 72.446 | 0.22086 | 945 | ||
| Synonymous | -1.22 | 106 | 91.1 | 1.16 | 0.00000521 | 906 |
| Loss of Function | 5.15 | 0 | 30.9 | 0.00 | 0.00000163 | 344 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.0000088 | 0.0000088 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: One of the major pre-mRNA-binding proteins. Binds tenaciously to poly(C) sequences. Likely to play a role in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. Can also bind poly(C) single- stranded DNA. Plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. When sumoylated, acts as a transcriptional coactivator of p53/TP53, playing a role in p21/CDKN1A and 14-3-3 sigma/SFN induction (By similarity). As far as transcription repression is concerned, acts by interacting with long intergenic RNA p21 (lincRNA-p21), a non-coding RNA induced by p53/TP53. This interaction is necessary for the induction of apoptosis, but not cell cycle arrest. {ECO:0000250, ECO:0000269|PubMed:16360036, ECO:0000269|PubMed:20673990, ECO:0000269|PubMed:22825850}.;
- Disease
- DISEASE: Au-Kline syndrome (AUKS) [MIM:616580]: A disorder characterized by intellectual disability, facial dysmorphism, cardiac defects, and connective tissue and skeletal abnormalities. Dysmorphic features include long palpebral fissures, ptosis, a broad prominent nasal bridge, hypoplastic alae nasi, an open downturned mouth, ears with underdeveloped and thick helices, high palate, and a unique tongue with a prominent median crease. Hypotonia, hyporeflexia, and high pain tolerance are additional features. {ECO:0000269|PubMed:26173930}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.673
Intolerance Scores
- RVIS EVS
- -0.21
- RVIS percentile EVS
- 38.28
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.787
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |