HNRNPF

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

Basic information

Region (hg38): 10:43385616-43409186

Previous symbols: [ "HNRPF" ]

Links

ENSG00000169813 ∙ NCBI:3185 ∙ OMIM:601037 ∙ HGNC:5039 ∙ Uniprot:P52597 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Inborn genetic diseases (4 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HNRNPF 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in HNRNPF

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

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

Position	Type	Phenotype	Significance	ClinVar
10-43386645-A-C		not specified	Uncertain significance (Apr 25, 2023)
10-43386779-T-C		not specified	Uncertain significance (Nov 17, 2022)
10-43387072-C-A		not specified	Uncertain significance (Sep 20, 2023)
10-43387104-C-T			Uncertain significance (Feb 08, 2023)
10-43387166-T-C		not specified	Uncertain significance (Feb 15, 2023)
10-43387227-T-C		not specified	Uncertain significance (Nov 08, 2022)
10-43387250-C-G			Uncertain significance (Jun 07, 2022)
10-43387840-G-A		not specified	Likely benign (Oct 05, 2023)
10-43387862-C-A		not specified	Uncertain significance (Nov 06, 2023)
10-43387875-C-A		not specified	Uncertain significance (Mar 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HNRNPF	protein_coding	protein_coding	ENST00000443950	1	23550

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.964	0.0358	125741	0	4	125745	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.94	113	241	0.468	0.0000143	2751
Missense in Polyphen		14	73.642	0.19011		899
Synonymous	-2.47	133	101	1.31	0.00000731	811
Loss of Function	2.98	0	10.4	0.00	5.19e-7	140

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)	0.0000705	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the heterogeneous nuclear ribonucleoprotein (hnRNP) complexes which provide the substrate for the processing events that pre-mRNAs undergo before becoming functional, translatable mRNAs in the cytoplasm. Plays a role in the regulation of alternative splicing events. Binds G-rich sequences in pre-mRNAs and keeps target RNA in an unfolded state. {ECO:0000269|PubMed:20526337}.
• Pathway: MECP2 and Associated Rett Syndrome;Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation;FGFR2 alternative splicing;Signaling by FGFR2;Signal Transduction;Signaling by FGFR;Metabolism of RNA;mRNA Splicing - Major Pathway;Signaling by Receptor Tyrosine Kinases;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.479

Intolerance Scores

• loftool: 0.296
• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.91

Haploinsufficiency Scores

• pHI: 0.131
• hipred: Y
• hipred_score: 0.818
• ghis: 0.663

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.980

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hnrnpf

Gene ontology

• Biological process: mRNA splicing, via spliceosome;RNA processing;fibroblast growth factor receptor signaling pathway;RNA metabolic process;interleukin-12-mediated signaling pathway;regulation of RNA splicing
• Cellular component: nucleus;nucleoplasm;cytosol;plasma membrane;membrane;catalytic step 2 spliceosome
• Molecular function: RNA binding;single-stranded RNA binding;protein binding;TBP-class protein binding