ZNF674

protein-coding

zinc 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]

Previous symbols:
  • MRX92

MANE transcript

NM_001190417.2

Inheritance

XL

ClinVar variants

U:72B:24

Top phenotype

Mental retardation, X-linked 92

gnomAD constraint

pLI —, LoF o/e 0.79

Max pathogenic AF

—

Genomic locus

chrX:46,497,725-46,545,457

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~47.7 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

X-linked intellectual disabilityNO_KNOWN

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.

intellectual disabilityNO_KNOWN

Inheritance Pattern: XL

Disease ID:MONDO:0001071

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Mental retardation, X-linked 92XL

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

Refs: 16385466; 23871722Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZNF674 variants in ClinVar

4 Conditions Cataloged
not specifiedTotal: 64
not providedTotal: 17
ZNF674-related disorderTotal: 11
History of neurodevelopmental disorderTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
10
clinvar
12
missense
64
clinvar
5
clinvar
5
clinvar
74
nonsense
1
clinvar
2
clinvar
3
start loss
0
frameshift
2
clinvar
2
splice donor/acceptor (+/-2bp)
5
clinvar
5
Total007219596
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001190417.2RefSeqNP_001177346.14MANE Select
ENST00000683375.1EnsemblENSP00000506769.14MANE Select
NM_001039891.3RefSeqNP_001034980.14Standard
NM_001146291.2RefSeqNP_001139763.14Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.061561980.7890.00001333861
Missense (PolyPhen)4865.2370.735781283
Synonymous0.5506671.90.9170.000005301015
Loss of Function0.7171113.90.7929.54e-7307

Population LoF Frequency

PopulationCAFp-valueStatus
African0.00240.0018notable
Latino/Admixed American0.00210.0015notable
Ashkenazi Jewish0.00600.0042notable
East Asian0.000450.00033rare
Finnish0.00130.00088notable
European (Non-Finnish)0.00680.0039notable
South Asian0.00280.0015notable
Other0.00430.0028notable

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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