ZNF674
protein-codingzinc finger protein 674, the group of Zinc fingers C2H2-type
Gene summary
This gene encodes a zinc finger protein with an N-terminal Kruppel-associated box-containing (KRAB) domain and 11 Kruppel-type C2H2 zinc finger domains. Like other zinc finger proteins, this gene may function as a transcription factor. This gene resides on an area of chromosome X that has been implicated in nonsyndromic X-linked cognitive disabilities. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2017]
- MRX92
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~47.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: XL
Disease ID:MONDO:0100284
Submitter: ClinGen
ZNF674 was first reported in relation to X-linked intellecutal disability in 2006 (Lugtenberg et al., PMID: 16385466). These authors identified three unique variants in the ZNF674 gene in three unrelated families with X-linked intellectual disability, including two missense variants and a stop-gained variant. However, there is insufficient evidence for the pathogenicity of these variants: one of the families with a missense variant also carried a translocation that co-segregated with the phenotype, the other missense variant was common in the general population, and stop-gained and other predicted null variants are also common in the general population, as noted by Piton et al. (2013) (PMID: 23871722). Delphin et al. (2012) also reported two patients with deletions encompassing the ZNF674 gene who did not have intellectual disability (PMID: 22126752). No experimental evidence linking variation in the ZNF674 gene to intellectual disability was identified. In summary, the evidence supporting the relationship between ZNF674 and X-linked intellectual disability has been disputed and no valid evidence remains to support the claim. More evidence is needed to either support or entirely refute the role ZNF674 plays in this disease. This classification was approved by the ClinGen Intellectual Disability and Autism Gene Curation Expert Panel on 5/4/2021.
Inheritance Pattern: XL
Disease ID:MONDO:0001071
Submitter: Ambry Genetics
Clinical Genomic Database (CGD)
Manifestation: Neurologic
Intervention: General
Rationale: 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
Comments: The evidence of variants as being related to disease causation has been questioned due to subsequent population-based studies
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ZNF674 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001190417.2. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 10 | 12 | |||
| missense | 64 | 5 | 5 | 74 | ||
| nonsense | 1 | 2 | 3 | |||
| start loss | 0 | |||||
| frameshift | 2 | 2 | ||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 72 | 19 | 5 | 96 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001177346.1 | 4 | MANE Select | |
| Ensembl | ENSP00000506769.1 | 4 | MANE Select | |
| RefSeq | NP_001034980.1 | 4 | Standard | |
| RefSeq | NP_001139763.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- regulation of transcription by RNA polymerase II
- negative regulation of transcription, DNA-templated
Molecular Function
- DNA-binding transcription factor activity, RNA polymerase II-specific
- DNA binding
- metal ion binding
Cellular Component
- nucleus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000523374
- Coding exons
- 4
- Length
- 47731
- Individuals with no LoFs
- 125068
- Homozygous LoFs
- 235
- Heterozygous LoFs
- 424
- Defined
- 125727
- p
- 0.00262
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.06 | 156 | 198 | 0.789 | 0.0000133 | 3861 |
| Missense (PolyPhen) | 48 | 65.237 | 0.73578 | 1283 | ||
| Synonymous | 0.550 | 66 | 71.9 | 0.917 | 0.00000530 | 1015 |
| Loss of Function | 0.717 | 11 | 13.9 | 0.792 | 9.54e-7 | 307 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0024 | 0.0018 | notable |
| Latino/Admixed American | 0.0021 | 0.0015 | notable |
| Ashkenazi Jewish | 0.0060 | 0.0042 | notable |
| East Asian | 0.00045 | 0.00033 | rare |
| Finnish | 0.0013 | 0.00088 | notable |
| European (Non-Finnish) | 0.0068 | 0.0039 | notable |
| South Asian | 0.0028 | 0.0015 | notable |
| Other | 0.0043 | 0.0028 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May be involved in transcriptional regulation.;
Intolerance Scores
- LoFtool
- 0.810
- RVIS EVS
- 1.04
- RVIS percentile EVS
- 91.26
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.00277
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |