ZNF446

zinc finger protein 446, the group of Zinc fingers C2H2-type|SCAN domain containing

Basic information

Region (hg38): 19:58474017-58481230

Links

ENSG00000083838 ∙ NCBI:55663 ∙ ∙ HGNC:21036 ∙ Uniprot:Q9NWS9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF446 gene.

• not_specified (92 variants)
• Short_stature (3 variants)
• not_provided (2 variants)
• High_myopia (1 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF446 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000017908.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			93	3		96
nonsense	1					1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	1	0	93	5	0

Highest pathogenic variant AF is 0.000028522143

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF446	protein_coding	protein_coding	ENST00000594369	6	7214

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.67e-8	0.660	125663	0	80	125743	0.000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.583	312	284	1.10	0.0000179	2835
Missense in Polyphen		80	75.902	1.054		819
Synonymous	-1.54	144	122	1.18	0.00000777	960
Loss of Function	1.20	14	19.8	0.708	0.00000110	191

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000308	0.000297
Ashkenazi Jewish	0.00	0.00
East Asian	0.000493	0.000489
Finnish	0.000188	0.000185
European (Non-Finnish)	0.000456	0.000440
Middle Eastern	0.000493	0.000489
South Asian	0.000229	0.000229
Other	0.000334	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Intolerance Scores

• loftool: 0.807
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.49

Haploinsufficiency Scores

• pHI: 0.0348
• hipred: N
• hipred_score: 0.146
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.733

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Zfp446

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: extracellular space;nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding