HMGN1
Basic information
Region (hg38): 21:39342314-39349647
Previous symbols: [ "HMG14" ]
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 HMGN1 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 | 5 | |||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 5 | 1 | 0 |
Variants in HMGN1
This is a list of pathogenic ClinVar variants found in the HMGN1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
21-39343130-T-C | Likely benign (May 24, 2018) | |||
21-39343143-T-C | not specified | Uncertain significance (Feb 22, 2023) | ||
21-39343153-C-G | not specified | Uncertain significance (Mar 15, 2024) | ||
21-39345187-C-T | not specified | Uncertain significance (Feb 17, 2022) | ||
21-39345208-C-T | not specified | Uncertain significance (Dec 21, 2022) | ||
21-39345211-C-T | not specified | Uncertain significance (Nov 15, 2021) | ||
21-39348336-G-A | not specified | Uncertain significance (May 30, 2024) | ||
21-39348435-G-C | not specified | Uncertain significance (Jun 11, 2024) | ||
21-39348438-G-C | not specified | Uncertain significance (Dec 28, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
HMGN1 | protein_coding | protein_coding | ENST00000380749 | 6 | 7333 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.207 | 0.755 | 125739 | 0 | 9 | 125748 | 0.0000358 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -1.37 | 79 | 51.4 | 1.54 | 0.00000252 | 635 |
Missense in Polyphen | 10 | 6.8152 | 1.4673 | 108 | ||
Synonymous | -1.56 | 30 | 20.9 | 1.43 | 0.00000119 | 180 |
Loss of Function | 1.73 | 2 | 6.90 | 0.290 | 2.90e-7 | 103 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000289 | 0.0000289 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.0000463 | 0.0000462 |
European (Non-Finnish) | 0.0000451 | 0.0000439 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000654 | 0.0000653 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Binds to the inner side of the nucleosomal DNA thus altering the interaction between the DNA and the histone octamer. May be involved in the process which maintains transcribable genes in a unique chromatin conformation. Inhibits the phosphorylation of nucleosomal histones H3 and H2A by RPS6KA5/MSK1 and RPS6KA3/RSK2 (By similarity). {ECO:0000250}.;
- Pathway
- Herpes simplex infection - Homo sapiens (human);ATM Signaling Network in Development and Disease;p38 MAPK Signaling Pathway;DNA Repair;p38 mapk signaling pathway;Formation of TC-NER Pre-Incision Complex;Dual incision in TC-NER;Gap-filling DNA repair synthesis and ligation in TC-NER;Transcription-Coupled Nucleotide Excision Repair (TC-NER);Nucleotide Excision Repair
(Consensus)
Recessive Scores
- pRec
- 0.0789
Intolerance Scores
- loftool
- 0.362
- rvis_EVS
- 0.3
- rvis_percentile_EVS
- 72.01
Haploinsufficiency Scores
- pHI
- 0.467
- hipred
- Y
- hipred_score
- 0.629
- ghis
- 0.543
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.778
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hmgn1
- Phenotype
- cellular phenotype; homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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); neoplasm;
Gene ontology
- Biological process
- pyrimidine dimer repair by nucleotide-excision repair;transcription-coupled nucleotide-excision repair;chromatin organization;regulation of transcription by RNA polymerase II;response to UV-B;response to UV-C;positive regulation of DNA-templated transcription, elongation;regulation of development, heterochronic;post-embryonic camera-type eye morphogenesis;regulation of epithelial cell proliferation;positive regulation of NAD+ ADP-ribosyltransferase activity
- Cellular component
- chromatin;nucleus;nucleoplasm;cytoplasm
- Molecular function
- DNA binding;nucleosomal DNA binding