HNRNPC
heterogeneous nuclear ribonucleoprotein C, the group of Spliceosomal C complex|RNA binding motif containing|Spliceosomal P complex|Heterogeneous nuclear ribonucleoproteins
Basic information
Region (hg38): 14:21209136-21269494
Previous symbols: [ "HNRPC" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Intellectual developmental disorder, autosomal dominant 74 | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Neurologic | 37541189 |
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the HNRNPC 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 | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 11 | 0 | 0 |
Variants in HNRNPC
This is a list of pathogenic ClinVar variants found in the HNRNPC region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 14-21211228-AGTCATCCTCGCCATTGGCGCTGTCTCT-A | Intellectual developmental disorder, autosomal dominant 74 | Pathogenic (Jan 31, 2024) | ||
| 14-21211419-C-G | Inborn genetic diseases | Uncertain significance (Dec 26, 2023) | ||
| 14-21211449-TC-T | Intellectual developmental disorder, autosomal dominant 74 | Pathogenic (Jan 31, 2024) | ||
| 14-21211476-C-G | Inborn genetic diseases | Uncertain significance (Aug 08, 2023) | ||
| 14-21211480-C-G | Inborn genetic diseases | Uncertain significance (Feb 07, 2023) | ||
| 14-21211524-C-A | Inborn genetic diseases | Uncertain significance (Feb 15, 2023) | ||
| 14-21211813-C-T | Inborn genetic diseases | Uncertain significance (Jun 22, 2021) | ||
| 14-21211821-C-T | Inborn genetic diseases | Uncertain significance (Feb 22, 2023) | ||
| 14-21211912-C-T | Inborn genetic diseases | Uncertain significance (Oct 14, 2023) | ||
| 14-21213018-C-A | Uncertain significance (May 23, 2024) | |||
| 14-21213049-C-T | Inborn genetic diseases | Uncertain significance (Dec 03, 2021) | ||
| 14-21213082-G-A | Inborn genetic diseases | Uncertain significance (Oct 16, 2024) | ||
| 14-21230326-A-G | Inborn genetic diseases | Uncertain significance (Dec 03, 2024) | ||
| 14-21230382-C-T | Intellectual developmental disorder, autosomal dominant 74 | Uncertain significance (Feb 12, 2024) | ||
| 14-21231020-T-A | HNRNPC-related condition | Uncertain significance (Mar 29, 2024) | ||
| 14-21234081-G-A | Inborn genetic diseases | Uncertain significance (Mar 31, 2024) | ||
| 14-21234129-T-C | Inborn genetic diseases | Uncertain significance (Apr 05, 2023) | ||
| 14-21234174-T-C | Uncertain significance (Jul 27, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HNRNPC | protein_coding | protein_coding | ENST00000320084 | 7 | 60359 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.978 | 0.0223 | 125231 | 0 | 17 | 125248 | 0.0000679 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.89 | 70 | 179 | 0.391 | 0.0000103 | 2007 |
| Missense in Polyphen | 5 | 34.403 | 0.14534 | 491 | ||
| Synonymous | -1.06 | 74 | 63.3 | 1.17 | 0.00000350 | 572 |
| Loss of Function | 3.48 | 1 | 16.1 | 0.0622 | 9.62e-7 | 185 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000579 | 0.000577 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000441 | 0.0000441 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000493 | 0.000492 |
dbNSFP
Source:
- Function
- FUNCTION: Binds pre-mRNA and nucleates the assembly of 40S hnRNP particles (PubMed:8264621). Interacts with poly-U tracts in the 3'-UTR or 5'-UTR of mRNA and modulates the stability and the level of translation of bound mRNA molecules (PubMed:12509468, PubMed:16010978, PubMed:7567451, PubMed:8264621). Single HNRNPC tetramers bind 230-240 nucleotides. Trimers of HNRNPC tetramers bind 700 nucleotides (PubMed:8264621). May play a role in the early steps of spliceosome assembly and pre-mRNA splicing. N6- methyladenosine (m6A) has been shown to alter the local structure in mRNAs and long non-coding RNAs (lncRNAs) via a mechanism named 'm(6)A-switch', facilitating binding of HNRNPC, leading to regulation of mRNA splicing (PubMed:25719671). {ECO:0000269|PubMed:12509468, ECO:0000269|PubMed:16010978, ECO:0000269|PubMed:25719671, ECO:0000269|PubMed:7567451, ECO:0000269|PubMed:8264621}.;
- Pathway
- Spliceosome - Homo sapiens (human);mRNA Processing;SUMOylation of RNA binding proteins;Post-translational protein modification;SUMO E3 ligases SUMOylate target proteins;Metabolism of proteins;Metabolism of RNA;mRNA Splicing - Major Pathway;SUMOylation;Regulation of Telomerase;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Recessive Scores
- pRec
- 0.281
Intolerance Scores
- loftool
- 0.379
- rvis_EVS
- -0.08
- rvis_percentile_EVS
- 47.79
Haploinsufficiency Scores
- pHI
- 0.162
- hipred
- N
- hipred_score
- 0.380
- ghis
- 0.523
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.995
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hnrnpc
- Phenotype
- embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Gene ontology
- Biological process
- mRNA splicing, via spliceosome;osteoblast differentiation;RNA splicing;RNA metabolic process;negative regulation of telomere maintenance via telomerase;ATP-dependent chromatin remodeling;3'-UTR-mediated mRNA stabilization
- Cellular component
- nuclear chromatin;extracellular region;nucleus;nucleoplasm;spliceosomal complex;telomerase holoenzyme complex;cytosol;actin cytoskeleton;membrane;protein-containing complex;extracellular exosome;catalytic step 2 spliceosome
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;RNA polymerase II distal enhancer sequence-specific DNA binding;RNA binding;mRNA 3'-UTR binding;protein binding;poly(U) RNA binding;nucleosomal DNA binding;identical protein binding;telomerase RNA binding;N6-methyladenosine-containing RNA binding