HNRNPL

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

Basic information

Region (hg38): 19:38836370-38852347

Previous symbols: [ "HNRPL" ]

Links

ENSG00000104824 ∙ NCBI:3191 ∙ OMIM:603083 ∙ HGNC:5045 ∙ Uniprot:P14866 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AR

ClinVar

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

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.

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				1	3	4
missense			26			26
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	27	1	5

Variants in HNRNPL

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

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

Position	Type	Phenotype	Significance	ClinVar
19-38836726-G-A		not specified	Uncertain significance (Mar 11, 2025)
19-38837396-T-G		not specified	Uncertain significance (May 04, 2022)
19-38837399-G-C		not specified	Uncertain significance (Aug 12, 2024)
19-38837413-A-G		not specified	Uncertain significance (Jul 14, 2023)
19-38837645-C-T		not specified	Uncertain significance (Jan 30, 2024)
19-38838491-G-T		not specified	Uncertain significance (May 11, 2022)
19-38838506-T-C		not specified	Uncertain significance (Jul 05, 2024)
19-38838538-G-A			Likely benign (Oct 01, 2022)
19-38838574-C-T		not specified	Uncertain significance (Dec 28, 2024)
19-38838877-C-T			Benign (Sep 16, 2021)
19-38838966-T-C		not specified	Uncertain significance (Dec 31, 2024)
19-38840128-T-C		not specified	Uncertain significance (Dec 14, 2024)
19-38840188-T-C		not specified	Uncertain significance (Jun 28, 2024)
19-38840194-C-A		not specified	Uncertain significance (Dec 02, 2024)
19-38840312-G-C		not specified	Uncertain significance (Jun 01, 2023)
19-38840319-G-C		not specified	Uncertain significance (Dec 23, 2024)
19-38840365-C-T		not specified	Uncertain significance (Sep 25, 2023)
19-38840551-C-T		not specified	Uncertain significance (Oct 03, 2024)
19-38843856-T-C		not specified	Uncertain significance (Apr 07, 2023)
19-38843907-C-T		not specified	Uncertain significance (Aug 20, 2024)
19-38845640-C-G			Benign (May 29, 2018)
19-38845854-G-A		not specified	Uncertain significance (Jul 13, 2021)
19-38845928-C-T			Benign (Jul 16, 2018)
19-38845938-G-C		not specified	Uncertain significance (Jul 25, 2023)
19-38849723-C-A		not specified	Uncertain significance (Jan 16, 2024)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

• 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