HNRNPR

heterogeneous nuclear ribonucleoprotein R, the group of RNA binding motif containing|Heterogeneous nuclear ribonucleoproteins

Basic information

Region (hg38): 1:23303771-23344336

Previous symbols: [ "HNRPR" ]

Links

ENSG00000125944

∙ NCBI:10236 ∙ OMIM:607201 ∙ HGNC:5047 ∙ Uniprot:O43390 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

neurodevelopmental disorder with dysmorphic facies and skeletal and brain abnormalities (Strong), mode of inheritance: AD
syndromic intellectual disability (Definitive), mode of inheritance: AD
neurodevelopmental disorder with dysmorphic facies and skeletal and brain abnormalities (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with dysmorphic facies and skeletal and brain abnormalities	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	31079900

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HNRNPR gene.

Inborn_genetic_diseases (38 variants)
not_provided (26 variants)
Neurodevelopmental_disorder_with_dysmorphic_facies_and_skeletal_and_brain_abnormalities (7 variants)
HNRNPR-related_disorder (2 variants)
not_specified (1 variants)
See_cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HNRNPR gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005826.5. 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						0
missense	1 clinvar		53 clinvar	5 clinvar		59
nonsense		2 clinvar	1 clinvar			3
start loss						0
frameshift	4 clinvar		2 clinvar			6
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	5	2	58	5	0

Highest pathogenic variant AF is 6.84261e-7

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HNRNPR	protein_coding	protein_coding	ENST00000374616	10	40566

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000647	125575	0	173	125748	0.000688

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.54	174	364	0.478	0.0000200	4143
Missense in Polyphen		30	116.58	0.25734		1504
Synonymous	0.927	112	125	0.895	0.00000682	1213
Loss of Function	4.74	2	30.0	0.0667	0.00000145	398

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00278	0.00258
Ashkenazi Jewish	0.00	0.00
East Asian	0.000611	0.000598
Finnish	0.000851	0.000832
European (Non-Finnish)	0.000814	0.000791
Middle Eastern	0.000611	0.000598
South Asian	0.0000995	0.0000980
Other	0.00101	0.000978

dbNSFP

Source: dbNSFP

Function: FUNCTION: Component of ribonucleosomes, which are complexes of at least 20 other different heterogenious nuclear ribonucleoproteins (hnRNP). hnRNP play an important role in processing of precursor mRNA in the nucleus.;
Pathway: mRNA Processing;Metabolism of RNA;mRNA Splicing - Major Pathway;EGFR1;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

pRec: 0.276

Intolerance Scores

loftool: 0.0907
rvis_EVS: -0.45
rvis_percentile_EVS: 24

Haploinsufficiency Scores

pHI: 0.991
hipred: Y
hipred_score: 0.783
ghis: 0.725

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.942

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Hnrnpr
Phenotype

Zebrafish Information Network

Gene name: hnrnpr
Affected structure: CaP motoneuron
Phenotype tag: abnormal
Phenotype quality: increased branchiness

Gene ontology

Biological process: mRNA splicing, via spliceosome;mRNA processing;circadian rhythm;RNA metabolic process;negative regulation of catalytic activity;mRNA destabilization
Cellular component: nucleus;nucleoplasm;spliceosomal complex;nucleolus;endoplasmic reticulum;dendrite;growth cone;axon terminus;catalytic step 2 spliceosome;ribonucleoprotein complex
Molecular function: RNA binding;mRNA binding;mRNA 3'-UTR binding;protein binding