HNRNPA3

heterogeneous nuclear ribonucleoprotein A3, the group of RNA binding motif containing|Heterogeneous nuclear ribonucleoproteins|MicroRNA protein coding host genes

Basic information

Region (hg38): 2:177212693-177223959

Previous symbols: [ "HNRPA3" ]

Links

ENSG00000170144 ∙ NCBI:220988 ∙ OMIM:605372 ∙ HGNC:24941 ∙ Uniprot:P51991 ∙ 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 HNRNPA3 gene.

• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HNRNPA3 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in HNRNPA3

This is a list of pathogenic ClinVar variants found in the HNRNPA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-177212837-A-C		not specified	Uncertain significance (May 31, 2023)
2-177216062-A-G		not specified	Uncertain significance (Oct 06, 2023)
2-177217783-G-C		not specified	Uncertain significance (Aug 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HNRNPA3	protein_coding	protein_coding	ENST00000392524	10	11396

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.995	0.00457	125742	0	2	125744	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.64	63	212	0.297	0.0000110	2439
Missense in Polyphen		5	39.822	0.12556		593
Synonymous	-1.37	81	66.7	1.21	0.00000331	721
Loss of Function	3.98	1	20.4	0.0491	0.00000102	269

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: Plays a role in cytoplasmic trafficking of RNA. Binds to the cis-acting response element, A2RE. May be involved in pre-mRNA splicing. {ECO:0000269|PubMed:11886857}.
• Pathway: Spliceosome - Homo sapiens (human);Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.0925

Intolerance Scores

• loftool: 0.198
• rvis_EVS: -0.27
• rvis_percentile_EVS: 33.97

Haploinsufficiency Scores

• pHI: 0.361
• hipred: Y
• hipred_score: 0.718
• ghis: 0.675

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hnrnpa3

Gene ontology

• Biological process: mRNA splicing, via spliceosome;RNA metabolic process;mRNA transport
• Cellular component: nucleus;nucleoplasm;cytoplasm;postsynaptic density;ribonucleoprotein granule;neuron projection;catalytic step 2 spliceosome;messenger ribonucleoprotein complex;ribonucleoprotein complex
• Molecular function: RNA binding;mRNA binding;protein binding;RNA transmembrane transporter activity