ZNF496

zinc finger protein 496, the group of Zinc fingers C2H2-type|SCAN domain containing

Basic information

Region (hg38): 1:247297412-247331867

Links

ENSG00000162714 ∙ NCBI:84838 ∙ OMIM:613911 ∙ HGNC:23713 ∙ Uniprot:Q96IT1 ∙ 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 ZNF496 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF496 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			54	2		56
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	54	2	0

Variants in ZNF496

This is a list of pathogenic ClinVar variants found in the ZNF496 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-247300529-T-C		not specified	Uncertain significance (Dec 13, 2023)
1-247300608-C-T		not specified	Uncertain significance (Feb 17, 2024)
1-247300631-C-T		not specified	Uncertain significance (Jan 16, 2024)
1-247300661-C-T		not specified	Uncertain significance (Jul 13, 2022)
1-247300784-G-A		not specified	Uncertain significance (Aug 10, 2021)
1-247300791-C-G		not specified	Uncertain significance (Jul 07, 2022)
1-247300793-C-T		not specified	Uncertain significance (Aug 19, 2024)
1-247300795-C-A		not specified	Uncertain significance (Sep 26, 2024)
1-247300802-A-G		not specified	Uncertain significance (Dec 06, 2021)
1-247300848-G-C		not specified	Uncertain significance (Oct 11, 2024)
1-247300877-C-T		not specified	Uncertain significance (Mar 21, 2023)
1-247300898-G-T		not specified	Uncertain significance (Sep 26, 2022)
1-247300941-C-T		not specified	Uncertain significance (Jun 02, 2023)
1-247300962-C-T		not specified	Uncertain significance (Nov 28, 2023)
1-247301045-T-C		not specified	Uncertain significance (Feb 22, 2023)
1-247301075-T-C		not specified	Uncertain significance (Jan 02, 2024)
1-247301180-C-A		not specified	Uncertain significance (Feb 26, 2024)
1-247301193-C-A		not specified	Uncertain significance (Sep 09, 2024)
1-247301264-G-A		not specified	Uncertain significance (Apr 09, 2024)
1-247308483-G-A		not specified	Uncertain significance (Oct 01, 2024)
1-247308507-G-A		not specified	Uncertain significance (Jun 28, 2023)
1-247308513-G-A		not specified	Uncertain significance (Feb 21, 2024)
1-247308543-C-A		not specified	Uncertain significance (Jan 16, 2024)
1-247309731-T-G		not specified	Uncertain significance (Mar 14, 2023)
1-247309753-C-T		not specified	Uncertain significance (Mar 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF496	protein_coding	protein_coding	ENST00000294753	7	34435

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00376	125741	0	4	125745	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.40	314	392	0.802	0.0000267	3842
Missense in Polyphen		97	146.29	0.66306		1395
Synonymous	-0.590	174	164	1.06	0.0000113	1168
Loss of Function	4.29	2	25.3	0.0791	0.00000117	266

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: DNA-binding transcription factor that can both act as an activator and a repressor. {ECO:0000250}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.213
• rvis_EVS: -1.44
• rvis_percentile_EVS: 3.95

Haploinsufficiency Scores

• pHI: 0.235
• hipred: Y
• hipred_score: 0.530
• ghis: 0.618

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.991

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zkscan17
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;positive regulation of transcription, DNA-templated
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;metal ion binding