NHLH1
Basic information
Region (hg38): 1:160367071-160372846
Previous symbols: [ "HEN1" ]
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 NHLH1 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 | 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 | 0 | 0 |
Variants in NHLH1
This is a list of pathogenic ClinVar variants found in the NHLH1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-160370816-G-A | not specified | Uncertain significance (Jan 17, 2024) | ||
| 1-160370837-G-A | Uncertain significance (Jul 01, 2024) | |||
| 1-160370855-G-A | not specified | Uncertain significance (Aug 09, 2021) | ||
| 1-160370883-G-C | not specified | Uncertain significance (Nov 29, 2021) | ||
| 1-160370937-G-C | not specified | Uncertain significance (Jul 13, 2021) | ||
| 1-160370952-C-G | not specified | Uncertain significance (Jan 10, 2023) | ||
| 1-160370964-C-T | not specified | Uncertain significance (Feb 14, 2025) | ||
| 1-160371032-C-A | not specified | Uncertain significance (May 02, 2024) | ||
| 1-160371119-G-A | not specified | Uncertain significance (Oct 12, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NHLH1 | protein_coding | protein_coding | ENST00000302101 | 1 | 5782 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.257 | 0.648 | 120825 | 0 | 2 | 120827 | 0.00000828 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.04 | 71 | 100 | 0.708 | 0.00000804 | 824 |
| Missense in Polyphen | 16 | 29.58 | 0.54091 | 196 | ||
| Synonymous | 0.0858 | 46 | 46.7 | 0.984 | 0.00000353 | 311 |
| Loss of Function | 1.23 | 1 | 3.48 | 0.287 | 2.80e-7 | 31 |
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) | 0.00000935 | 0.00000930 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000336 | 0.0000329 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May serve as DNA-binding protein and may be involved in the control of cell-type determination, possibly within the developing nervous system.;
Recessive Scores
- pRec
- 0.203
Intolerance Scores
- loftool
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 52.85
Haploinsufficiency Scores
- pHI
- 0.370
- hipred
- Y
- hipred_score
- 0.665
- ghis
- 0.567
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nhlh1
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); 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); 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);
Gene ontology
- Biological process
- regulation of transcription by RNA polymerase II;central nervous system development;cell differentiation;positive regulation of transcription by RNA polymerase II
- Cellular component
- nucleus
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;protein dimerization activity