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

• intellectual disability, autosomal dominant 40 (Definitive), mode of inheritance: AD
• neurodevelopmental disorder with dysmorphic facies and skeletal and brain abnormalities (Strong), mode of inheritance: AD
• syndromic intellectual disability (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 (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.

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			21	2		23
nonsense		2	1			3
start loss						0
frameshift	1		2			3
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region				1		1
non coding			1			1
Total	1	2	26	2	0

Variants in HNRNPR

This is a list of pathogenic ClinVar variants found in the HNRNPR region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-23310525-A-C		Inborn genetic diseases	Uncertain significance (Mar 30, 2024)
1-23310548-G-A		HNRNPR-related disorder	Uncertain significance (Aug 19, 2022)
1-23310587-T-A		See cases	Uncertain significance (Jul 17, 2020)
1-23310602-C-T		Neurodevelopmental disorder with dysmorphic facies and skeletal and brain abnormalities	Pathogenic (Oct 13, 2022)
1-23310681-G-A		Inborn genetic diseases	Uncertain significance (Mar 01, 2024)
1-23310696-T-C		Inborn genetic diseases	Likely benign (Apr 28, 2023)
1-23310702-G-A		Inborn genetic diseases • Neurodevelopmental disorder with dysmorphic facies and skeletal and brain abnormalities	Likely pathogenic (May 29, 2015)
1-23310705-G-A			Likely pathogenic (Aug 16, 2021)
1-23310712-A-AC		Neurodevelopmental disorder with dysmorphic facies and skeletal and brain abnormalities	Pathogenic (Oct 13, 2022)
1-23310755-G-GC		Neurodevelopmental disorder with dysmorphic facies and skeletal and brain abnormalities	Pathogenic (Oct 13, 2022)
1-23310756-C-A		Inborn genetic diseases	Uncertain significance (Apr 19, 2023)
1-23310755-G-GCC		Inborn genetic diseases	Pathogenic (Aug 14, 2023)
1-23310830-C-T		Inborn genetic diseases	Uncertain significance (Oct 03, 2022)
1-23310869-C-A		Inborn genetic diseases	Uncertain significance (Jun 02, 2024)
1-23310926-T-C			Uncertain significance (Apr 01, 2024)
1-23310998-C-G		Inborn genetic diseases	Likely benign (May 06, 2024)
1-23311020-T-C		Inborn genetic diseases	Likely benign (Jun 22, 2023)
1-23311201-G-A		Neurodevelopmental disorder with dysmorphic facies and skeletal and brain abnormalities	Uncertain significance (Jul 06, 2023)
1-23311201-G-C		Inborn genetic diseases	Uncertain significance (May 27, 2022)
1-23311280-T-C			Uncertain significance (Nov 01, 2024)
1-23311326-T-C		Inborn genetic diseases	Likely benign (Aug 19, 2021)
1-23313632-T-C			Uncertain significance (May 30, 2021)
1-23313672-T-A		Inborn genetic diseases	Uncertain significance (Feb 12, 2024)
1-23318578-G-A			Uncertain significance (Jun 18, 2024)
1-23318588-T-TTG		Inborn genetic diseases	Uncertain significance (Feb 23, 2022)

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

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