HNRNPK

protein-coding

heterogeneous 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]

Previous symbols:
  • HNRPK

MANE transcript

NM_031263.4

Inheritance

AD

ClinVar variants

P:85U:112B:59

Top phenotype

Au-Kline syndrome

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr9:83,968,083-83,980,631

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~12.5 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Au-Kline syndromeSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014700

Submitter: Labcorp Genetics (formerly Invitae)

Au-Kline syndromeDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0014700

Submitter: G2P

neurodevelopmental disorder-craniofacial dysmorphism-cardiac defect-hip dysplasia syndromeDEFINITIVE

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).

Au-Kline syndromeSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014700

Submitter: PanelApp Australia

Au-Kline syndromeSTRONG

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).

Au-Kline syndromeMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0014700

Submitter: Ambry Genetics

Au-Kline syndromeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0014700

Submitter: Orphanet

Clinical Genomic Database (CGD)

Au-Kline syndromeAD

Manifestation: Cardiovascular; Craniofacial; Musculoskeletal; Neurologic

Intervention: Cardiovascular

Rationale: The condition can involve congenital cardiac anomalies, and awareness may allow early management

Refs: 26173930Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to HNRNPK variants in ClinVar

11 Conditions Cataloged
not providedTotal: 233
Au-Kline syndromeTotal: 86
not specifiedTotal: 35
Inborn genetic diseasesTotal: 35
HNRNPK-related disorderTotal: 9
HNRNPK-related disordersTotal: 7
Congenital heart diseaseTotal: 1
Generalized hypotoniaTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
45
clinvar
2
clinvar
49
missense
3
clinvar
30
clinvar
97
clinvar
11
clinvar
1
clinvar
142
nonsense
4
clinvar
6
clinvar
10
start loss
0
frameshift
18
clinvar
7
clinvar
1
clinvar
26
splice donor/acceptor (+/-2bp)
9
clinvar
8
clinvar
12
clinvar
29
Total3451112563256

Highest pathogenic variant AF is 0.0000065725476

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 209 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_031263.4RefSeqNP_112553.115MANE Select
ENST00000376263.8EnsemblENSP00000365439.315MANE Select
NM_001318186.2RefSeqNP_001305115.114Standard
NM_001318187.2RefSeqNP_001305116.114Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense3.99932810.3300.00001623016
Missense (PolyPhen)1672.4460.22086945
Synonymous-1.2210691.11.160.00000521906
Loss of Function5.15030.90.000.00000163344

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.00000880.0000088rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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