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.

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.

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					1	1
missense			44	2		46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	2	1

Variants in ZNF90

This is a list of pathogenic ClinVar variants found in the ZNF90 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-20104242-C-T		not specified	Uncertain significance (Dec 26, 2023)
19-20104257-G-T		not specified	Uncertain significance (Apr 06, 2024)
19-20104344-T-A		not specified	Uncertain significance (Jun 12, 2023)
19-20104344-T-C		not specified	Uncertain significance (Sep 01, 2021)
19-20104350-C-A		not specified	Likely benign (Sep 01, 2021)
19-20105235-A-G		not specified	Uncertain significance (Oct 18, 2021)
19-20105274-C-G		not specified	Uncertain significance (Mar 01, 2023)
19-20105275-C-T		not specified	Uncertain significance (Aug 30, 2021)
19-20105283-G-T		not specified	Uncertain significance (Apr 23, 2024)
19-20105310-T-C		not specified	Likely benign (Apr 13, 2023)
19-20117807-C-A		not specified	Uncertain significance (Apr 17, 2024)
19-20117823-G-T		not specified	Uncertain significance (Sep 14, 2022)
19-20117856-C-T		not specified	Uncertain significance (Jul 08, 2022)
19-20117868-A-G		not specified	Uncertain significance (Nov 10, 2022)
19-20117893-A-T		not specified	Likely benign (Jun 17, 2024)
19-20117915-G-C		not specified	Uncertain significance (Jun 04, 2024)
19-20117920-G-A			Benign (Aug 02, 2017)
19-20117985-T-A		not specified	Uncertain significance (Oct 26, 2021)
19-20118041-C-A		not specified	Uncertain significance (Mar 14, 2023)
19-20118042-A-G		not specified	Uncertain significance (Nov 02, 2023)
19-20118068-C-G		not specified	Uncertain significance (Jan 19, 2024)
19-20118089-G-A		not specified	Uncertain significance (Oct 06, 2021)
19-20118116-C-G		not specified	Uncertain significance (Jun 16, 2024)
19-20118206-T-G		not specified	Uncertain significance (Nov 06, 2023)
19-20118239-T-C		not specified	Uncertain significance (Apr 19, 2024)

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