ZFHX3
Basic information
Region (hg38): 16:72782884-73891871
Previous symbols: [ "ATBF1", "C16orf47" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (143 variants)
- not provided (76 variants)
- Neurodevelopmental disorder (6 variants)
- not specified (4 variants)
- Autism spectrum disorder (2 variants)
- Intellectual disability (1 variants)
- Prostate cancer, somatic (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZFHX3 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 | 25 | 16 | 43 | |||
missense | 139 | 14 | 14 | 167 | ||
nonsense | 5 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
inframe indel | 11 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region ? | 1 | 1 | ||||
non coding ? | 0 | |||||
Total | 0 | 5 | 144 | 42 | 36 |
Variants in ZFHX3
This is a list of pathogenic ClinVar variants found in the ZFHX3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
16-72787228-T-G | not specified | Uncertain significance (Aug 02, 2021) | ||
16-72787301-C-T | not specified | Uncertain significance (Jan 30, 2024) | ||
16-72787302-G-A | Likely benign (May 01, 2022) | |||
16-72787355-C-T | not specified | Uncertain significance (Jul 06, 2021) | ||
16-72787404-A-G | ZFHX3-related disorder | Benign/Likely benign (Oct 01, 2022) | ||
16-72787423-G-A | not specified | Uncertain significance (Jul 12, 2023) | ||
16-72787435-C-G | not specified | Uncertain significance (Sep 20, 2023) | ||
16-72787444-T-A | not specified | Uncertain significance (Aug 08, 2023) | ||
16-72787445-G-A | ZFHX3-related disorder | Benign (Dec 31, 2019) | ||
16-72787446-G-C | ZFHX3-related disorder | Benign (Nov 16, 2019) | ||
16-72787477-G-A | not specified | Uncertain significance (May 08, 2023) | ||
16-72787482-A-C | ZFHX3-related disorder | Likely benign (Jul 10, 2019) | ||
16-72787494-G-C | not specified | Uncertain significance (Mar 31, 2023) | ||
16-72787591-G-C | not specified | Uncertain significance (Aug 10, 2023) | ||
16-72787627-G-A | not specified | Uncertain significance (Feb 27, 2024) | ||
16-72787648-G-C | not specified | Uncertain significance (Feb 13, 2023) | ||
16-72787693-G-C | not specified | Uncertain significance (Apr 25, 2022) | ||
16-72787694-AGCC-A | ZFHX3-related disorder | Benign (Jan 06, 2020) | ||
16-72787694-AGCCGCC-A | ZFHX3-related disorder | Benign (Sep 10, 2019) | ||
16-72787694-AGCCGCCGCC-A | ZFHX3-related disorder | Benign (Aug 05, 2019) | ||
16-72787694-A-AGCC | ZFHX3-related disorder | Benign (Jun 27, 2019) | ||
16-72787694-A-AGCCGCC | ZFHX3-related disorder | Benign (Dec 06, 2019) | ||
16-72787697-C-A | not specified | Uncertain significance (Apr 03, 2023) | ||
16-72787701-GCCGCCGCCGCCGCCGCCA-G | ZFHX3-related disorder | Benign/Likely benign (Mar 01, 2023) | ||
16-72787707-GCCGCCGCCGCCA-G | ZFHX3-related disorder | Likely benign (May 15, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ZFHX3 | protein_coding | protein_coding | ENST00000268489 | 9 | 276814 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 1.39e-13 | 125706 | 0 | 42 | 125748 | 0.000167 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -1.23 | 2279 | 2.12e+3 | 1.08 | 0.000128 | 24335 |
Missense in Polyphen | 553 | 640.33 | 0.86362 | 7621 | ||
Synonymous | -6.30 | 1171 | 927 | 1.26 | 0.0000650 | 7409 |
Loss of Function | 9.52 | 10 | 125 | 0.0801 | 0.00000673 | 1418 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000218 | 0.000214 |
Ashkenazi Jewish | 0.000204 | 0.000198 |
East Asian | 0.000184 | 0.000163 |
Finnish | 0.000198 | 0.000185 |
European (Non-Finnish) | 0.000226 | 0.000211 |
Middle Eastern | 0.000184 | 0.000163 |
South Asian | 0.000206 | 0.000163 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional regulator which can act as an activator or a repressor. Inhibits the enhancer element of the AFP gene by binding to its AT-rich core sequence. In concert with SMAD- dependent TGF-beta signaling can repress the transcription of AFP via its interaction with SMAD2/3 (PubMed:25105025). Regulates the circadian locomotor rhythms via transcriptional activation of neuropeptidergic genes which are essential for intercellular synchrony and rhythm amplitude in the suprachiasmatic nucleus (SCN) of the brain (By similarity). Regulator of myoblasts differentiation through the binding to the AT-rich sequence of MYF6 promoter and promoter repression (PubMed:11312261). Down- regulates the MUC5AC promoter in gastric cancer (PubMed:17330845). In association with RUNX3, upregulates CDKN1A promoter activity following TGF-beta stimulation (PubMed:20599712). Inhibits estrogen receptor (ESR1) function by selectively competing with coactivator NCOA3 for binding to ESR1 in ESR1-positive breast cancer cells (PubMed:20720010). {ECO:0000250|UniProtKB:Q61329, ECO:0000269|PubMed:11312261, ECO:0000269|PubMed:17330845, ECO:0000269|PubMed:20599712, ECO:0000269|PubMed:20720010, ECO:0000269|PubMed:25105025}.;
- Pathway
- Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);fibrinolysis pathway;intrinsic prothrombin activation pathway;C-MYB transcription factor network;extrinsic prothrombin activation pathway
(Consensus)
Recessive Scores
- pRec
- 0.155
Intolerance Scores
- loftool
- 0.0860
- rvis_EVS
- -4.26
- rvis_percentile_EVS
- 0.12
Haploinsufficiency Scores
- pHI
- 0.746
- hipred
- Y
- hipred_score
- 0.595
- ghis
- 0.603
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.890
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | High | High | High |
Primary Immunodeficiency | High | High | High |
Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Zfhx3
- Phenotype
- neoplasm; 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; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); renal/urinary system phenotype; 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); growth/size/body region phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;regulation of transcription, DNA-templated;transcription by RNA polymerase II;brain development;muscle organ development;circadian regulation of gene expression;regulation of neuron differentiation;positive regulation of cell adhesion;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;response to transforming growth factor beta;regulation of locomotor rhythm
- Cellular component
- nucleus;nucleoplasm;transcription factor complex;cytoplasm;nuclear body
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;zinc ion binding;enzyme binding;transcription regulatory region DNA binding