H1-0
Basic information
Region (hg38): 22:37805229-37807432
Previous symbols: [ "H1FV", "H1F0" ]
Links
Phenotypes
GenCC
Source:
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 H1-0 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 | 1 | |||||
| missense | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 1 | 0 |
Variants in H1-0
This is a list of pathogenic ClinVar variants found in the H1-0 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 22-37805549-C-T | not specified | Uncertain significance (Apr 14, 2022) | ||
| 22-37805566-G-A | not specified | Likely benign (Dec 05, 2024) | ||
| 22-37805592-C-T | Likely benign (Apr 01, 2022) | |||
| 22-37805774-C-G | not specified | Uncertain significance (Jan 24, 2024) | ||
| 22-37805803-G-A | not specified | Uncertain significance (Oct 25, 2024) | ||
| 22-37805869-A-G | not specified | Uncertain significance (Oct 17, 2023) | ||
| 22-37805884-A-G | not specified | Likely benign (Aug 01, 2024) | ||
| 22-37805893-G-A | not specified | Uncertain significance (Dec 22, 2023) | ||
| 22-37805918-A-G | not specified | Uncertain significance (Jul 14, 2021) | ||
| 22-37805923-A-G | not specified | Uncertain significance (Aug 07, 2024) | ||
| 22-37805948-C-A | not specified | Uncertain significance (May 05, 2023) | ||
| 22-37805969-C-T | not specified | Uncertain significance (Dec 15, 2022) | ||
| 22-37806022-C-T | not specified | Uncertain significance (Oct 12, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| H1-0 | protein_coding | protein_coding | ENST00000340857 | 1 | 2329 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.643 | 0.333 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.878 | 88 | 114 | 0.769 | 0.00000634 | 1250 |
| Missense in Polyphen | 13 | 25.122 | 0.51748 | 303 | ||
| Synonymous | -1.32 | 64 | 51.9 | 1.23 | 0.00000320 | 405 |
| Loss of Function | 1.69 | 0 | 3.31 | 0.00 | 1.37e-7 | 74 |
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) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Histones H1 are necessary for the condensation of nucleosome chains into higher-order structures. The H1F0 histones are found in cells that are in terminal stages of differentiation or that have low rates of cell division.;
- Pathway
- apoptotic dna-fragmentation and tissue homeostasis;Formation of Senescence-Associated Heterochromatin Foci (SAHF);DNA Damage/Telomere Stress Induced Senescence;Cellular Senescence;Cellular responses to stress;Activation of DNA fragmentation factor;Apoptosis induced DNA fragmentation;Apoptotic execution phase;Apoptosis;Programmed Cell Death;Cellular responses to external stimuli
(Consensus)
Recessive Scores
- pRec
- 0.208
Intolerance Scores
- loftool
- 0.0891
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 49.39
Haploinsufficiency Scores
- pHI
- 0.850
- hipred
- Y
- hipred_score
- 0.775
- ghis
- 0.615
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.988
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- H1f0
- Phenotype
- endocrine/exocrine gland phenotype; growth/size/body region phenotype; embryo phenotype; immune system phenotype; hematopoietic system phenotype; reproductive system 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); normal phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;apoptotic DNA fragmentation;nucleosome assembly;chromatin silencing;regulation of transcription, DNA-templated;nucleosome positioning;chromosome condensation;negative regulation of chromatin silencing;negative regulation of DNA recombination;positive regulation of transcription regulatory region DNA binding
- Cellular component
- nucleosome;nuclear chromatin;nucleus;nucleoplasm;nuclear euchromatin;Golgi apparatus;actin cytoskeleton;nuclear body;transcriptional repressor complex
- Molecular function
- AT DNA binding;double-stranded DNA binding;RNA binding;protein binding;chromatin DNA binding;nucleosomal DNA binding