HNRNPD
heterogeneous nuclear ribonucleoprotein D, the group of Heterogeneous nuclear ribonucleoproteins|RNA binding motif containing
Basic information
Region (hg38): 4:82352498-82374503
Previous symbols: [ "AUF1", "HNRPD" ]
Links
Phenotypes
GenCC
Source:
- neurodevelopmental disorder (Moderate), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (30 variants)
- HNRNPD-related_disorder (3 variants)
- not_provided (2 variants)
- Intellectual_disability (2 variants)
- Neurodevelopmental_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the HNRNPD gene is commonly pathogenic or not. These statistics are base on transcript: NM_000031370.3. 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | |||||
| missense | 30 | 30 | ||||
| nonsense | 2 | |||||
| start loss | 0 | |||||
| frameshift | 3 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 1 | 3 | 31 | 2 | 0 |
Highest pathogenic variant AF is 0.000001299437
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HNRNPD | protein_coding | protein_coding | ENST00000313899 | 8 | 22006 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.996 | 0.00379 | 125738 | 0 | 4 | 125742 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.45 | 91 | 185 | 0.492 | 0.00000885 | 2316 |
| Missense in Polyphen | 16 | 69.378 | 0.23062 | 890 | ||
| Synonymous | 1.48 | 50 | 65.1 | 0.768 | 0.00000342 | 648 |
| Loss of Function | 4.03 | 1 | 20.9 | 0.0479 | 0.00000106 | 253 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000353 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Binds with high affinity to RNA molecules that contain AU-rich elements (AREs) found within the 3'-UTR of many proto- oncogenes and cytokine mRNAs. Also binds to double- and single- stranded DNA sequences in a specific manner and functions a transcription factor. Each of the RNA-binding domains specifically can bind solely to a single-stranded non-monotonous 5'-UUAG-3' sequence and also weaker to the single-stranded 5'-TTAGGG-3' telomeric DNA repeat. Binds RNA oligonucleotides with 5'-UUAGGG-3' repeats more tightly than the telomeric single-stranded DNA 5'- TTAGGG-3' repeats. Binding of RRM1 to DNA inhibits the formation of DNA quadruplex structure which may play a role in telomere elongation. May be involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. May play a role in the regulation of the rhythmic expression of circadian clock core genes. Directly binds to the 3'UTR of CRY1 mRNA and induces CRY1 rhythmic translation. May also be involved in the regulation of PER2 translation. {ECO:0000269|PubMed:10080887, ECO:0000269|PubMed:11051545, ECO:0000269|PubMed:24423872}.;
- Pathway
- mRNA Processing;AUF1 (hnRNP D0) binds and destabilizes mRNA;Metabolism of RNA;mRNA Splicing - Major Pathway;Regulation of mRNA stability by proteins that bind AU-rich elements;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Recessive Scores
- pRec
- 0.426
Intolerance Scores
- loftool
- 0.160
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 52.85
Haploinsufficiency Scores
- pHI
- 0.212
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.724
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.903
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Hnrnpd
- Phenotype
- cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); renal/urinary system phenotype; immune system phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- mRNA splicing, via spliceosome;liver development;regulation of transcription, DNA-templated;RNA processing;RNA catabolic process;RNA metabolic process;cerebellum development;regulation of telomere maintenance;regulation of circadian rhythm;regulation of mRNA stability;positive regulation of translation;positive regulation of transcription, DNA-templated;mRNA stabilization;response to calcium ion;response to electrical stimulus;3'-UTR-mediated mRNA destabilization;cellular response to amino acid stimulus;cellular response to estradiol stimulus;cellular response to nitric oxide;circadian regulation of translation;response to rapamycin;positive regulation of telomere capping;response to sodium phosphate;cellular response to putrescine;positive regulation of telomerase RNA reverse transcriptase activity;hepatocyte dedifferentiation
- Cellular component
- nucleus;nucleoplasm;cytosol;synapse;ribonucleoprotein complex
- Molecular function
- AT DNA binding;chromatin binding;RNA binding;mRNA binding;protein binding;transcription factor binding;mRNA 3'-UTR AU-rich region binding;telomeric DNA binding;histone deacetylase binding;sequence-specific DNA binding;sequence-specific double-stranded DNA binding