ZNF200

zinc finger protein 200, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 16:3222325-3236221

Links

ENSG00000010539 ∙ ∙ OMIM:603231 ∙ HGNC:12993 ∙ Uniprot:P98182 ∙ 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 ZNF200 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF200 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						0
missense			38	1		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	1	0

Variants in ZNF200

This is a list of pathogenic ClinVar variants found in the ZNF200 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-3223922-G-T		not specified	Uncertain significance (Nov 14, 2024)
16-3223929-T-C		not specified	Uncertain significance (Mar 11, 2024)
16-3223936-G-A		not specified	Uncertain significance (Dec 20, 2023)
16-3223938-C-T		not specified	Uncertain significance (Mar 08, 2025)
16-3223992-G-C		not specified	Uncertain significance (Mar 29, 2023)
16-3224074-A-G		not specified	Uncertain significance (Mar 04, 2024)
16-3224097-C-G		not specified	Uncertain significance (Feb 16, 2023)
16-3224112-C-T		not specified	Uncertain significance (Aug 11, 2024)
16-3224113-G-A		not specified	Uncertain significance (Jul 25, 2023)
16-3224128-G-A		not specified	Uncertain significance (Dec 15, 2023)
16-3224160-G-A		not specified	Uncertain significance (Jul 22, 2024)
16-3224161-G-T		not specified	Uncertain significance (Jan 27, 2025)
16-3224170-C-T		not specified	Uncertain significance (Feb 09, 2025)
16-3224181-C-T		not specified	Uncertain significance (May 08, 2023)
16-3224241-T-C		not specified	Uncertain significance (Jan 09, 2024)
16-3224278-T-C		not specified	Uncertain significance (Apr 15, 2024)
16-3224322-G-A		not specified	Uncertain significance (Dec 19, 2022)
16-3224322-G-C		not specified	Uncertain significance (Dec 06, 2022)
16-3224344-G-A		not specified	Uncertain significance (Jun 26, 2024)
16-3224349-C-T		not specified	Uncertain significance (Jun 09, 2022)
16-3224361-A-G		not specified	Uncertain significance (Mar 01, 2025)
16-3224469-C-T		not specified	Uncertain significance (Feb 01, 2023)
16-3224601-C-G		not specified	Uncertain significance (Nov 21, 2024)
16-3224610-A-C		not specified	Uncertain significance (Aug 12, 2024)
16-3232438-C-G		not specified	Uncertain significance (Sep 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF200	protein_coding	protein_coding	ENST00000431561	4	13897

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000180	0.685	125695	0	53	125748	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.49	273	212	1.29	0.0000107	2614
Missense in Polyphen		57	53.588	1.0637		663
Synonymous	-1.59	95	77.3	1.23	0.00000377	739
Loss of Function	1.10	11	15.7	0.701	9.73e-7	187

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000293	0.000293
Ashkenazi Jewish	0.00	0.00
East Asian	0.000761	0.000761
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.000761	0.000761
South Asian	0.000294	0.000294
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Could have a role in spermatogenesis.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.948
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.91

Haploinsufficiency Scores

• pHI: 0.123
• hipred: N
• hipred_score: 0.112
• ghis: 0.500

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.538

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;biological_process
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;molecular_function;nucleic acid binding;metal ion binding