ZNF408
Basic information
Region (hg38): 11:46701030-46705912
Links
Phenotypes
GenCC
Source:
- retinitis pigmentosa (Supportive), mode of inheritance: AD
- exudative vitreoretinopathy (Supportive), mode of inheritance: AD
- exudative vitreoretinopathy 6 (Limited), mode of inheritance: AD
- retinitis pigmentosa 72 (Moderate), mode of inheritance: AR
- exudative vitreoretinopathy 6 (Strong), mode of inheritance: AD
- retinitis pigmentosa 72 (Strong), mode of inheritance: AR
- exudative vitreoretinopathy 6 (Strong), mode of inheritance: AD
- retinitis pigmentosa 72 (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Exudative vitreoretinopathy 6; Retinitis pigmentosa 72 | AD/AR | 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 | Ophthalmologic | 6897033; 23716654; 25882705 |
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 ZNF408 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 | 128 | 139 | ||||
missense | 300 | 310 | ||||
nonsense | 10 | 12 | ||||
start loss | 1 | |||||
frameshift | 15 | 16 | ||||
inframe indel | 8 | |||||
splice donor/acceptor (+/-2bp) | 3 | |||||
splice region | 3 | 8 | 11 | |||
non coding | 13 | 16 | ||||
Total | 0 | 6 | 341 | 146 | 12 |
Variants in ZNF408
This is a list of pathogenic ClinVar variants found in the ZNF408 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
11-46701049-T-C | Uncertain significance (Nov 15, 2022) | |||
11-46701051-G-A | Uncertain significance (Jun 16, 2020) | |||
11-46701052-A-T | Uncertain significance (Apr 02, 2021) | |||
11-46701067-T-C | Uncertain significance (Dec 20, 2019) | |||
11-46701073-T-C | Uncertain significance (Nov 28, 2019) | |||
11-46701077-G-C | Uncertain significance (Oct 31, 2019) | |||
11-46701078-G-A | Uncertain significance (Jun 27, 2022) | |||
11-46701080-G-A | Likely benign (Dec 08, 2017) | |||
11-46701082-A-G | ZNF408-related disorder | Likely benign (Dec 15, 2023) | ||
11-46701083-G-C | Uncertain significance (Jan 10, 2020) | |||
11-46701090-C-T | Likely benign (Dec 26, 2020) | |||
11-46701091-T-A | Uncertain significance (Jul 15, 2019) | |||
11-46701092-G-A | Likely benign (Apr 08, 2021) | |||
11-46701093-C-T | Uncertain significance (Nov 23, 2023) | |||
11-46701095-A-G | Likely benign (Jan 18, 2024) | |||
11-46701098-C-T | Likely benign (Nov 03, 2022) | |||
11-46701099-G-A | Uncertain significance (Dec 06, 2023) | |||
11-46701109-C-T | Likely benign (Mar 12, 2022) | |||
11-46701118-C-T | Likely benign (Dec 20, 2022) | |||
11-46701135-G-C | not specified | Likely benign (-) | ||
11-46701181-T-C | Benign (May 16, 2021) | |||
11-46701385-C-T | Likely benign (Dec 16, 2023) | |||
11-46701386-C-T | Likely benign (Jul 21, 2022) | |||
11-46701387-TTC-T | Likely benign (Feb 01, 2022) | |||
11-46701389-C-T | Likely benign (Oct 25, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ZNF408 | protein_coding | protein_coding | ENST00000311764 | 5 | 5095 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00000118 | 0.988 | 125696 | 0 | 52 | 125748 | 0.000207 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.712 | 403 | 445 | 0.905 | 0.0000270 | 4583 |
Missense in Polyphen | 141 | 184.07 | 0.76601 | 1761 | ||
Synonymous | -0.249 | 190 | 186 | 1.02 | 0.0000104 | 1557 |
Loss of Function | 2.29 | 14 | 26.8 | 0.522 | 0.00000157 | 272 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000448 | 0.000448 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000219 | 0.000217 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.000271 | 0.000264 |
Middle Eastern | 0.000219 | 0.000217 |
South Asian | 0.000167 | 0.000163 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May be involved in transcriptional regulation.;
- Disease
- DISEASE: Retinitis pigmentosa 72 (RP72) [MIM:616469]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269|PubMed:25882705}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.0911
Intolerance Scores
- loftool
- 0.729
- rvis_EVS
- -1.02
- rvis_percentile_EVS
- 8.1
Haploinsufficiency Scores
- pHI
- 0.0671
- hipred
- N
- hipred_score
- 0.172
- ghis
- 0.511
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.947
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Zfp408
- Phenotype
- immune system phenotype; hematopoietic system phenotype;
Zebrafish Information Network
- Gene name
- znf408
- Affected structure
- ocular blood vessel
- Phenotype tag
- abnormal
- Phenotype quality
- morphology
Gene ontology
- Biological process
- regulation of transcription by RNA polymerase II
- Cellular component
- nucleus
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;identical protein binding;metal ion binding