ZNF518B

zinc finger protein 518B, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 4:10439880-10457426

Links

ENSG00000178163 ∙ NCBI:85460 ∙ OMIM:617734 ∙ HGNC:29365 ∙ Uniprot:Q9C0D4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF518B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF518B 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			93	4	1	98
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	93	5	1

Variants in ZNF518B

This is a list of pathogenic ClinVar variants found in the ZNF518B region.

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

Position	Type	Phenotype	Significance	ClinVar
4-10443114-T-C		not specified	Uncertain significance (Mar 02, 2023)
4-10443135-T-C		not specified	Uncertain significance (Jul 15, 2024)
4-10443231-T-A		not specified	Uncertain significance (Dec 10, 2024)
4-10443232-G-C		not specified	Uncertain significance (Apr 05, 2023)
4-10443237-G-A		not specified	Uncertain significance (Nov 07, 2024)
4-10443284-T-G		not specified	Uncertain significance (May 01, 2022)
4-10443312-T-C		not specified	Uncertain significance (Oct 29, 2024)
4-10443363-T-A		not specified	Uncertain significance (Sep 20, 2024)
4-10443445-C-T		not specified	Uncertain significance (Dec 03, 2024)
4-10443455-A-T		not specified	Uncertain significance (Jul 21, 2021)
4-10443513-C-T		not specified	Uncertain significance (Apr 24, 2024)
4-10443522-C-A		not specified	Uncertain significance (Jun 02, 2024)
4-10443538-C-A		not specified	Uncertain significance (Dec 16, 2023)
4-10443557-T-G		not specified	Uncertain significance (Nov 23, 2021)
4-10443573-A-C		not specified	Uncertain significance (Dec 15, 2023)
4-10443603-C-T		not specified	Likely benign (Jun 10, 2022)
4-10443604-G-A		not specified	Uncertain significance (Oct 02, 2023)
4-10443604-G-T		not specified	Uncertain significance (Sep 26, 2024)
4-10443626-G-C		not specified	Uncertain significance (Sep 10, 2024)
4-10443640-A-G		not specified	Uncertain significance (Jun 06, 2023)
4-10443645-T-G		not specified	Uncertain significance (Jan 23, 2024)
4-10443672-A-G		not specified	Uncertain significance (Apr 22, 2024)
4-10443688-A-C		not specified	Uncertain significance (Sep 14, 2021)
4-10443724-C-T		not specified	Uncertain significance (Sep 28, 2022)
4-10443730-G-C		not specified	Uncertain significance (Mar 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF518B	protein_coding	protein_coding	ENST00000326756	1	17537

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00229	0.998	125698	0	49	125747	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.92	672	546	1.23	0.0000293	7067
Missense in Polyphen		151	151.52	0.99658		1999
Synonymous	-3.38	270	208	1.30	0.0000117	2098
Loss of Function	3.31	10	29.4	0.340	0.00000144	451

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000387	0.000387
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000203	0.000202
Middle Eastern	0.00	0.00
South Asian	0.000359	0.000359
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.

Recessive Scores

• pRec: 0.0837

Intolerance Scores

• loftool: 0.553
• rvis_EVS: 0.66
• rvis_percentile_EVS: 84.2

Haploinsufficiency Scores

• pHI: 0.133
• hipred: N
• hipred_score: 0.273
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0846

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp518b

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