ZNF10

zinc finger protein 10, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 12:133130574-133159465

Links

ENSG00000256223 ∙ NCBI:7556 ∙ OMIM:194538 ∙ HGNC:12879 ∙ Uniprot:P21506 ∙ 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 ZNF10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF10 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			21	2		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	2	0

Variants in ZNF10

This is a list of pathogenic ClinVar variants found in the ZNF10 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-133151127-G-C		not specified	Uncertain significance (Mar 18, 2024)
12-133151831-T-A		not specified	Uncertain significance (Jan 23, 2023)
12-133151894-G-C		not specified	Uncertain significance (Apr 15, 2024)
12-133155525-C-G		not specified	Uncertain significance (Nov 15, 2023)
12-133155536-T-C		not specified	Uncertain significance (Jun 11, 2024)
12-133155651-G-T		not specified	Uncertain significance (May 30, 2023)
12-133155679-A-G		not specified	Uncertain significance (Mar 18, 2024)
12-133155734-T-A		not specified	Uncertain significance (May 10, 2022)
12-133155749-A-C		not specified	Uncertain significance (May 31, 2023)
12-133155772-C-T		not specified	Uncertain significance (Aug 30, 2021)
12-133155809-G-A		not specified	Likely benign (Aug 29, 2022)
12-133155878-A-G		not specified	Uncertain significance (Feb 23, 2023)
12-133155971-A-G		not specified	Uncertain significance (Oct 26, 2021)
12-133155985-C-T		not specified	Uncertain significance (May 24, 2023)
12-133156018-G-A		not specified	Uncertain significance (Jan 08, 2024)
12-133156025-A-G		not specified	Uncertain significance (May 12, 2024)
12-133156044-A-T		not specified	Uncertain significance (Jun 11, 2021)
12-133156121-C-T		not specified	Uncertain significance (Jan 26, 2023)
12-133156142-G-C		not specified	Uncertain significance (May 14, 2024)
12-133156451-T-A		not specified	Uncertain significance (Jan 26, 2022)
12-133156546-G-C		not specified	Uncertain significance (Jun 29, 2023)
12-133156583-C-G		not specified	Uncertain significance (May 23, 2023)
12-133156655-T-C		not specified	Uncertain significance (Dec 27, 2023)
12-133156729-G-C		not specified	Uncertain significance (Oct 26, 2021)
12-133156759-A-G		not specified	Uncertain significance (Oct 26, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF10	protein_coding	protein_coding	ENST00000248211	4	28891

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00160	0.993	125728	0	19	125747	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.24	234	294	0.796	0.0000138	3819
Missense in Polyphen		69	106.83	0.64587		1384
Synonymous	0.119	100	102	0.985	0.00000454	1018
Loss of Function	2.43	8	19.6	0.407	8.89e-7	283

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000188	0.000188
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000109	0.000109
Finnish	0.0000953	0.0000924
European (Non-Finnish)	0.0000625	0.0000615
Middle Eastern	0.000109	0.000109
South Asian	0.0000654	0.0000653
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)

Recessive Scores

• pRec: 0.0971

Intolerance Scores

• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.219
• hipred: N
• hipred_score: 0.168
• ghis: 0.561

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.579

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;protein binding;metal ion binding