ZNF124

zinc finger protein 124, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 1:247121975-247172020

Links

ENSG00000196418 ∙ NCBI:7678 ∙ OMIM:194631 ∙ HGNC:12907 ∙ Uniprot:Q15973 ∙ 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 ZNF124 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF124 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			20			20
nonsense					1	1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	0	1

Variants in ZNF124

This is a list of pathogenic ClinVar variants found in the ZNF124 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-247156608-T-G		not specified	Uncertain significance (Oct 25, 2023)
1-247156636-C-T		not specified	Uncertain significance (Feb 14, 2023)
1-247156645-G-A		not specified	Uncertain significance (Feb 07, 2023)
1-247156679-C-T		not specified	Uncertain significance (Jun 11, 2021)
1-247156733-T-C		not specified	Uncertain significance (Nov 22, 2023)
1-247156802-C-T		not specified	Uncertain significance (Aug 12, 2021)
1-247156803-G-T			Benign (Dec 31, 2019)
1-247156840-G-C		not specified	Uncertain significance (May 11, 2022)
1-247156885-A-G		not specified	Uncertain significance (Mar 23, 2023)
1-247156912-A-G		not specified	Uncertain significance (Oct 25, 2023)
1-247156933-C-A		not specified	Uncertain significance (Oct 03, 2022)
1-247156975-C-T		not specified	Uncertain significance (Mar 07, 2023)
1-247156976-G-A		not specified	Uncertain significance (Jun 19, 2024)
1-247157001-T-G		not specified	Uncertain significance (Jul 27, 2022)
1-247157009-G-C		not specified	Uncertain significance (May 14, 2024)
1-247157018-C-T		not specified	Uncertain significance (Mar 24, 2023)
1-247157056-C-T		not specified	Uncertain significance (Dec 20, 2023)
1-247157093-G-A		not specified	Uncertain significance (Mar 01, 2023)
1-247157134-C-T		not specified	Uncertain significance (Jun 18, 2021)
1-247157173-T-C		not specified	Uncertain significance (May 02, 2024)
1-247157208-C-G		not specified	Uncertain significance (Feb 28, 2024)
1-247159015-C-T		not specified	Uncertain significance (Feb 08, 2022)
1-247159050-G-T		not specified	Uncertain significance (Mar 24, 2023)
1-247159054-T-TC			Uncertain significance (Aug 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF124	protein_coding	protein_coding	ENST00000340684	4	50042

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0109	0.640	125712	0	18	125730	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.158	163	157	1.04	0.00000821	1938
Missense in Polyphen		54	53.342	1.0123		659
Synonymous	0.691	44	50.2	0.876	0.00000255	485
Loss of Function	0.420	3	3.89	0.770	1.64e-7	59

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000277	0.000277
European (Non-Finnish)	0.0000792	0.0000791
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)

Intolerance Scores

• loftool: 0.730
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.0877
• hipred: N
• hipred_score: 0.123
• ghis: 0.597

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.345

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Gm20541

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