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

ClinVar

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

• not provided (2 variants)
• Neurodevelopmental disorder with craniofacial dysmorphism and skeletal defects (1 variants)
• Inborn genetic diseases (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.

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					2	2
missense	2	1	22			25
nonsense		1				1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region					2	2
non coding			1	1		2
Total	2	2	25	1	2

Variants in HNRNPH1

This is a list of pathogenic ClinVar variants found in the HNRNPH1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-179615556-TTTGA-T			Uncertain significance (Mar 29, 2021)
5-179616089-ATAACTTACTCTAAGTACAGTAACAAACAGGCTTTACCG-A			Uncertain significance (Sep 10, 2019)
5-179616155-T-A			Uncertain significance (Jan 21, 2022)
5-179616182-T-TGCTG		Neurodevelopmental disorder with craniofacial dysmorphism and skeletal defects	Pathogenic (Mar 30, 2023)
5-179616196-G-A			Benign (Jul 27, 2018)
5-179616201-C-T			Uncertain significance (Oct 20, 2023)
5-179616202-G-A			Likely benign (Nov 01, 2024)
5-179616205-GCTGGA-G		Neurodevelopmental disorder with craniofacial dysmorphism and skeletal defects	Likely pathogenic (Oct 09, 2024)
5-179616220-TGTTAA-T			Benign (Jun 14, 2018)
5-179616923-C-G		Inborn genetic diseases	Uncertain significance (Oct 24, 2023)
5-179616950-A-G		Inborn genetic diseases	Uncertain significance (Jan 04, 2022)
5-179617032-C-T		Neurodevelopmental disorder with craniofacial dysmorphism and skeletal defects	Uncertain significance (Jun 10, 2023)
5-179617063-C-T		Inborn genetic diseases	Uncertain significance (Apr 07, 2023)
5-179617101-T-C			Uncertain significance (Sep 21, 2022)
5-179617108-G-C		Neurodevelopmental disorder with craniofacial dysmorphism and skeletal defects	Uncertain significance (Aug 30, 2023)
5-179617607-C-G			Uncertain significance (May 18, 2023)
5-179617615-A-T			Pathogenic (Oct 19, 2023)
5-179617637-G-A			Uncertain significance (Jan 01, 2023)
5-179617640-G-A		Inborn genetic diseases	Uncertain significance (Jul 30, 2024)
5-179617640-G-T			Uncertain significance (Jan 18, 2020)
5-179617822-C-T		HNRNPH1-related disorder	Uncertain significance (Feb 08, 2024)
5-179617839-C-T			Uncertain significance (Apr 19, 2024)
5-179617869-T-C		Inborn genetic diseases	Uncertain significance (Sep 14, 2023)
5-179617884-C-A			Uncertain significance (May 31, 2024)
5-179618003-T-A		Inborn genetic diseases	Uncertain significance (Apr 22, 2022)

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