ZNF431

zinc finger protein 431, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:21142023-21196053

Links

ENSG00000196705 ∙ NCBI:170959 ∙ OMIM:619505 ∙ HGNC:20809 ∙ Uniprot:Q8TF32 ∙ 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 ZNF431 gene.

• Inborn genetic diseases (17 variants)
• not specified (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF431 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				1		1
missense			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	2	0

Variants in ZNF431

This is a list of pathogenic ClinVar variants found in the ZNF431 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-21143563-T-C		not specified	Uncertain significance (Nov 14, 2023)
19-21143582-A-G		not specified	Uncertain significance (Dec 06, 2022)
19-21166407-C-A		not specified	Uncertain significance (Oct 25, 2023)
19-21167589-A-G		not specified	Uncertain significance (Apr 13, 2022)
19-21167611-G-A		not specified	Likely benign (Oct 11, 2021)
19-21182721-G-C		not specified	Uncertain significance (May 04, 2022)
19-21182743-G-T		not specified	Uncertain significance (May 04, 2022)
19-21182925-A-G		not specified	Uncertain significance (Jul 25, 2023)
19-21182932-G-A		not specified	Uncertain significance (Sep 26, 2023)
19-21182944-G-T		not specified	Likely benign (Nov 23, 2021)
19-21183084-A-C		not specified	Uncertain significance (Nov 10, 2022)
19-21183231-C-T		not specified	Uncertain significance (Feb 23, 2023)
19-21183263-A-T		not specified	Uncertain significance (Dec 22, 2023)
19-21183264-T-A		not specified	Uncertain significance (Apr 28, 2022)
19-21183294-C-T		not specified	Uncertain significance (Feb 26, 2024)
19-21183324-G-A		Malignant tumor of prostate	Uncertain significance (-)
19-21183370-T-G		not specified	Uncertain significance (Feb 22, 2023)
19-21183385-A-C		not specified	Uncertain significance (Aug 02, 2021)
19-21183403-C-A		not specified	Uncertain significance (Aug 23, 2021)
19-21183663-A-G		not specified	Uncertain significance (Jul 09, 2021)
19-21183724-A-G		not specified	Uncertain significance (Sep 14, 2021)
19-21183730-G-A		not specified	Uncertain significance (Jun 22, 2021)
19-21183750-C-A		not specified	Uncertain significance (Jun 22, 2021)
19-21183787-G-A		not specified	Uncertain significance (Feb 15, 2023)
19-21183964-A-T		not specified	Uncertain significance (May 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF431	protein_coding	protein_coding	ENST00000311048	5	48208

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0250	0.922	125715	0	12	125727	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.187	278	287	0.969	0.0000128	3822
Missense in Polyphen		93	109.29	0.85097		1507
Synonymous	1.02	85	97.8	0.869	0.00000434	983
Loss of Function	1.66	4	9.54	0.419	3.98e-7	136

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000330	0.0000330
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000151	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sequence-specific DNA binding transcriptional repressor. Represses target gene transcription by recruiting HDAC1 and HDAC2 histone deacetylases. Acts as a specific transcriptional repressor for PTCH1 during embryonic development. Required for osteoblast differentiation and sonic hedgehog/SHH signaling response. Binds to the consensus site 5'-GCGCCC-3' in the promoter of PTCH1 (By similarity). {ECO:0000250}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Intolerance Scores

• loftool: 0.779
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.41

Haploinsufficiency Scores

• pHI: 0.273
• hipred: N
• hipred_score: 0.132
• ghis: 0.468

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.395

Gene Damage Prediction

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

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;cell differentiation;negative regulation of DNA-binding transcription factor activity
• Cellular component: nucleus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;chromatin binding;metal ion binding