ZNF90

zinc finger protein 90, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:20077994-20127076

Links

ENSG00000213988 ∙ NCBI:7643 ∙ OMIM:603973 ∙ HGNC:13165 ∙ Uniprot:Q03938 ∙ 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 ZNF90 gene.

• not_specified (108 variants)
• not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF90 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000007138.2. 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					1	1
missense			103	5		108
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	103	5	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF90	protein_coding	protein_coding	ENST00000418063	4	49083

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00290	0.597	125611	0	58	125669	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.04	356	305	1.17	0.0000148	3929
Missense in Polyphen		90	100.5	0.89551		1376
Synonymous	-0.188	107	105	1.02	0.00000468	1046
Loss of Function	0.395	4	4.95	0.808	2.09e-7	62

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000963	0.0000932
Ashkenazi Jewish	0.00	0.00
East Asian	0.00250	0.00245
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.00250	0.00245
South Asian	0.000266	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.

Intolerance Scores

• rvis_EVS: 1.22
• rvis_percentile_EVS: 93.14

Haploinsufficiency Scores

• pHI: 0.0903
• hipred: N
• hipred_score: 0.112
• ghis: 0.494

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.200

Gene Damage Prediction

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

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;DNA-binding transcription factor activity;zinc ion binding