HNRNPH3

heterogeneous nuclear ribonucleoprotein H3, the group of RNA binding motif containing|Heterogeneous nuclear ribonucleoproteins

Basic information

Region (hg38): 10:68331174-68343193

Previous symbols: [ "HNRPH3" ]

Links

ENSG00000096746 ∙ NCBI:3189 ∙ OMIM:602324 ∙ HGNC:5043 ∙ Uniprot:P31942 ∙ 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 HNRNPH3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HNRNPH3 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in HNRNPH3

This is a list of pathogenic ClinVar variants found in the HNRNPH3 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-68337235-T-C		not specified	Uncertain significance (Dec 10, 2024)
10-68337866-A-G		not specified	Uncertain significance (Oct 03, 2024)
10-68337893-A-C		not specified	Uncertain significance (Mar 30, 2024)
10-68338585-G-A		not specified	Uncertain significance (Aug 14, 2023)
10-68338598-G-A		not specified	Uncertain significance (Mar 20, 2024)
10-68338619-G-T		not specified	Uncertain significance (Dec 25, 2024)
10-68338664-G-A		not specified	Uncertain significance (Sep 24, 2024)
10-68339181-G-A		not specified	Uncertain significance (Oct 26, 2022)
10-68339475-G-A		not specified	Uncertain significance (Sep 03, 2024)
10-68339529-C-T		not specified	Uncertain significance (Apr 01, 2022)
10-68339542-A-G		not specified	Uncertain significance (Aug 02, 2022)
10-68341214-T-C		not specified	Uncertain significance (Dec 02, 2024)
10-68341629-G-A		not specified	Uncertain significance (May 03, 2023)
10-68341679-G-C		not specified	Uncertain significance (Apr 01, 2024)
10-68341986-G-A		not specified	Uncertain significance (Dec 31, 2024)
10-68342002-G-T		not specified	Uncertain significance (Jan 24, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HNRNPH3	protein_coding	protein_coding	ENST00000265866	9	12018

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.992	0.00779	125688	0	4	125692	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.57	103	207	0.497	0.0000110	2258
Missense in Polyphen		4	17.806	0.22464		219
Synonymous	0.946	57	66.8	0.853	0.00000363	660
Loss of Function	4.09	2	23.3	0.0857	0.00000169	238

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)	0.0000358	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the splicing process and participates in early heat shock-induced splicing arrest. Due to their great structural variations the different isoforms may possess different functions in the splicing reaction.
• Pathway: TCR (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.486
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.292
• hipred: Y
• hipred_score: 0.783
• ghis: 0.654

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.991

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hnrnph3

Gene ontology

• Biological process: mRNA splicing, via spliceosome;RNA processing;RNA splicing;epithelial cell differentiation
• Cellular component: nucleus;nucleoplasm;spliceosomal complex
• Molecular function: RNA binding;protein binding