ZNF99

zinc finger protein 99, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:22752183-22784151

Previous symbols: [ "C19orf9" ]

Links

ENSG00000213973 ∙ NCBI:7652 ∙ OMIM:603981 ∙ HGNC:13175 ∙ Uniprot:A8MXY4 ∙ 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 ZNF99 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF99 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				6	1	7
missense			56	7		63
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	56	13	2

Variants in ZNF99

This is a list of pathogenic ClinVar variants found in the ZNF99 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-22757320-C-T		not specified	Likely benign (Dec 07, 2021)
19-22757327-T-C		not specified	Uncertain significance (Dec 07, 2021)
19-22757334-G-A		not specified	Uncertain significance (Apr 18, 2023)
19-22757345-T-G		not specified	Uncertain significance (Feb 10, 2022)
19-22757354-T-G		not specified	Uncertain significance (Jun 24, 2022)
19-22757390-A-AG			Benign (Oct 02, 2018)
19-22757409-A-C		not specified	Uncertain significance (Oct 20, 2021)
19-22757427-A-G		not specified	Uncertain significance (Nov 18, 2022)
19-22757504-G-A		not specified	Uncertain significance (Aug 05, 2022)
19-22757561-T-A		not specified	Uncertain significance (Oct 05, 2023)
19-22757615-T-C		not specified	Uncertain significance (Feb 13, 2024)
19-22757705-C-G		not specified	Uncertain significance (Apr 08, 2022)
19-22757752-A-G			Likely benign (Apr 01, 2023)
19-22757760-A-T		not specified	Uncertain significance (Dec 01, 2023)
19-22757766-T-G		not specified	Uncertain significance (Dec 28, 2022)
19-22757773-T-C			Likely benign (Apr 01, 2023)
19-22757840-G-A		not specified	Uncertain significance (Mar 04, 2024)
19-22757846-T-C		not specified	Uncertain significance (Mar 02, 2023)
19-22757859-T-C		not specified	Uncertain significance (May 24, 2024)
19-22757891-T-C		not specified	Likely benign (Jan 10, 2022)
19-22757978-G-C		not specified	Uncertain significance (Jun 14, 2024)
19-22757986-T-C		not specified	Uncertain significance (Jun 21, 2023)
19-22757993-T-C		not specified	Uncertain significance (Jan 10, 2023)
19-22758025-T-C			Benign (Oct 02, 2018)
19-22758075-G-T		not specified	Likely benign (Aug 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF99	protein_coding	protein_coding	ENST00000596209	4	27903

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0249	0.794	125582	0	2	125584	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.52	568	422	1.34	0.0000190	5723
Missense in Polyphen		179	151.47	1.1817		2162
Synonymous	-2.17	172	139	1.23	0.00000658	1417
Loss of Function	0.996	3	5.53	0.543	2.36e-7	65

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000638	0.0000621
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000887	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.128

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;metal ion binding