ZNF483

zinc finger protein 483, the group of Zinc fingers C2H2-type|SCAN domain containing

Basic information

Region (hg38): 9:111525158-111577844

Links

ENSG00000173258 ∙ NCBI:158399 ∙ ∙ HGNC:23384 ∙ Uniprot:Q8TF39 ∙ 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 ZNF483 gene.

• Inborn genetic diseases (21 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF483 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			19	2		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	0

Variants in ZNF483

This is a list of pathogenic ClinVar variants found in the ZNF483 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-111527483-A-G		not specified	Uncertain significance (Jul 12, 2022)
9-111527573-T-C		not specified	Uncertain significance (Jan 10, 2023)
9-111527628-A-G		not specified	Uncertain significance (Jul 09, 2021)
9-111527720-A-G		not specified	Uncertain significance (Jun 11, 2021)
9-111533745-A-G		not specified	Likely benign (Feb 02, 2022)
9-111534264-T-G		not specified	Uncertain significance (Nov 04, 2022)
9-111534306-T-G		not specified	Uncertain significance (Aug 02, 2023)
9-111541676-A-T		not specified	Uncertain significance (Jun 24, 2022)
9-111541677-A-G		not specified	Uncertain significance (Apr 11, 2023)
9-111541839-C-G		not specified	Uncertain significance (Dec 01, 2022)
9-111541863-A-C		not specified	Uncertain significance (Aug 08, 2023)
9-111541878-T-C		not specified	Uncertain significance (Jan 27, 2022)
9-111541924-G-A		not specified	Uncertain significance (Jul 13, 2022)
9-111541981-G-T		not specified	Uncertain significance (Aug 30, 2021)
9-111542020-A-G		not specified	Uncertain significance (Jul 11, 2023)
9-111542073-C-T		not specified	Uncertain significance (Apr 25, 2022)
9-111542128-T-C		not specified	Uncertain significance (Mar 01, 2023)
9-111542185-G-A		not specified	Uncertain significance (Jan 07, 2022)
9-111542208-G-A		not specified	Likely benign (Oct 12, 2021)
9-111542377-C-T		Inborn genetic diseases	Uncertain significance (Dec 03, 2021)
9-111542505-A-G		not specified	Uncertain significance (Jul 14, 2023)
9-111543019-A-G		not specified	Uncertain significance (Feb 27, 2023)
9-111543084-A-G		not specified	Uncertain significance (Oct 17, 2023)
9-111543148-G-A		not specified	Uncertain significance (Jan 30, 2024)
9-111563194-A-T		not specified	Uncertain significance (Oct 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF483	protein_coding	protein_coding	ENST00000309235	5	52686

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.967	0.0326	125735	0	10	125745	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.40	253	385	0.657	0.0000194	4910
Missense in Polyphen		25	45.37	0.55102		453
Synonymous	0.532	133	141	0.943	0.00000725	1366
Loss of Function	4.23	4	28.3	0.142	0.00000146	406

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000868	0.0000868
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000359	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
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: 0.602
• rvis_EVS: -0.69
• rvis_percentile_EVS: 14.97

Haploinsufficiency Scores

• pHI: 0.265
• hipred: N
• hipred_score: 0.380
• ghis: 0.623

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.651

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zkscan16

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