ZNF100

zinc finger protein 100, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:21722771-21767579

Links

ENSG00000197020 ∙ NCBI:163227 ∙ OMIM:603982 ∙ HGNC:12880 ∙ Uniprot:Q8IYN0 ∙ 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 ZNF100 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF100 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				7	1	8
missense			22	4	1	27
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	11	3

Variants in ZNF100

This is a list of pathogenic ClinVar variants found in the ZNF100 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-21726693-A-T		not specified	Uncertain significance (Aug 26, 2022)
19-21726694-G-C		not specified	Uncertain significance (Aug 02, 2021)
19-21726848-C-G		not specified	Uncertain significance (Sep 13, 2023)
19-21726881-C-A		not specified	Uncertain significance (Mar 21, 2024)
19-21726900-T-C		not specified	Uncertain significance (Dec 09, 2024)
19-21726954-C-T		not specified	Uncertain significance (Oct 01, 2024)
19-21726955-C-T		not specified	Uncertain significance (Dec 19, 2023)
19-21726978-G-T		not specified	Uncertain significance (Dec 04, 2024)
19-21726979-T-G		not specified	Uncertain significance (Dec 04, 2024)
19-21727008-C-G		not specified	Uncertain significance (Jun 24, 2022)
19-21727015-C-G		not specified	Uncertain significance (Oct 12, 2021)
19-21727055-A-G			Likely benign (Dec 01, 2023)
19-21727064-G-A			Likely benign (Dec 01, 2023)
19-21727073-G-A			Benign (Jan 19, 2018)
19-21727128-T-C		not specified	Uncertain significance (Nov 28, 2024)
19-21727218-A-G		not specified	Uncertain significance (Oct 01, 2024)
19-21727282-G-C		not specified	Uncertain significance (Jun 29, 2022)
19-21727299-A-G		not specified	Uncertain significance (Oct 01, 2024)
19-21727307-G-C		not specified	Uncertain significance (Oct 29, 2024)
19-21727311-G-A		not specified	Uncertain significance (Jul 07, 2024)
19-21727320-T-C		not specified	Uncertain significance (Sep 05, 2024)
19-21727320-T-G		not specified	Uncertain significance (Oct 01, 2024)
19-21727321-G-C		not specified	Uncertain significance (May 12, 2024)
19-21727321-G-T		not specified	Uncertain significance (Oct 01, 2024)
19-21727323-G-T			Benign (Apr 09, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF100	protein_coding	protein_coding	ENST00000358296	5	44863

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000189	0.490	125316	0	8	125324	0.0000319

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.822	316	277	1.14	0.0000130	3568
Missense in Polyphen		79	86.289	0.91553		1185
Synonymous	-2.07	122	96.2	1.27	0.00000458	931
Loss of Function	0.349	6	7.00	0.858	2.95e-7	88

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.00000882	0.00000881
Middle Eastern	0.000381	0.000381
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)

Intolerance Scores

• loftool: 0.707
• rvis_EVS: 1.35
• rvis_percentile_EVS: 94.4

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.112
• ghis: 0.434

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0588

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