HNRNPH1

heterogeneous nuclear ribonucleoprotein H1, the group of RNA binding motif containing|Heterogeneous nuclear ribonucleoproteins

Basic information

Region (hg38): 5:179614178-179634784

Previous symbols: [ "HNRPH1" ]

Links

ENSG00000169045 ∙ NCBI:3187 ∙ OMIM:601035 ∙ HGNC:5041 ∙ Uniprot:P31943 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder with craniofacial dysmorphism and skeletal defects (Strong), mode of inheritance: AD
• neurodevelopmental disorder (Strong), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HNRNPH1 gene.

• not_provided (44 variants)
• Inborn_genetic_diseases (18 variants)
• Neurodevelopmental_disorder_with_craniofacial_dysmorphism_and_skeletal_defects (8 variants)
• not_specified (2 variants)
• HNRNPH1-related_disorder (2 variants)
• Intellectual_disability,_X-linked,_syndromic,_Bain_type (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HNRNPH1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001257293.2. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4	2	6
missense	3	1	44			48
nonsense		1				1
start loss			1			1
frameshift	3	1	4			8
splice donor/acceptor (+/-2bp)			1			1
Total	6	3	50	4	2

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HNRNPH1	protein_coding	protein_coding	ENST00000356731	12	20607

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000664	125732	0	2	125734	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.09	74	259	0.285	0.0000134	2963
Missense in Polyphen		14	64.594	0.21674		814
Synonymous	-0.0754	90	89.1	1.01	0.00000495	826
Loss of Function	4.84	0	27.3	0.00	0.00000143	326

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)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This protein is a 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. Mediates pre-mRNA alternative splicing regulation. Inhibits, together with CUGBP1, insulin receptor (IR) pre-mRNA exon 11 inclusion in myoblast. Binds to the IR RNA. Binds poly(RG). {ECO:0000269|PubMed:11003644, ECO:0000269|PubMed:16946708}.
• Pathway: MECP2 and Associated Rett Syndrome;mRNA Processing;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)

Intolerance Scores

• loftool: 0.0638
• rvis_EVS: -0.27
• rvis_percentile_EVS: 33.97

Haploinsufficiency Scores

• pHI: 0.836
• hipred: Y
• hipred_score: 0.840
• ghis: 0.665

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.958

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hnrnph1
• Phenotype: hearing/vestibular/ear phenotype

Gene ontology

• Biological process: mRNA splicing, via spliceosome;RNA processing;fibroblast growth factor receptor signaling pathway;RNA metabolic process;regulation of RNA splicing
• Cellular component: nucleus;nucleoplasm;cytosol;membrane;catalytic step 2 spliceosome
• Molecular function: RNA binding;protein binding;poly(U) RNA binding