ZNF548

zinc finger protein 548, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:57389850-57403498

Links

ENSG00000188785 ∙ NCBI:147694 ∙ ∙ HGNC:26561 ∙ Uniprot:Q8NEK5 ∙ 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 ZNF548 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF548 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	3		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	3	0

Variants in ZNF548

This is a list of pathogenic ClinVar variants found in the ZNF548 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-57397048-G-A		not specified	Uncertain significance (Jun 10, 2024)
19-57397127-T-G		not specified	Uncertain significance (Mar 20, 2023)
19-57397132-C-T		not specified	Uncertain significance (Aug 01, 2022)
19-57397169-C-T		not specified	Uncertain significance (Nov 15, 2021)
19-57398595-A-G		not specified	Likely benign (Jul 13, 2022)
19-57398598-G-A		not specified	Uncertain significance (Oct 04, 2022)
19-57398603-C-A		not specified	Uncertain significance (Apr 06, 2022)
19-57398607-C-T		not specified	Uncertain significance (Dec 23, 2023)
19-57398816-G-A		not specified	Uncertain significance (Feb 11, 2022)
19-57398862-C-A		not specified	Uncertain significance (Dec 08, 2021)
19-57398923-T-G		not specified	Likely benign (Mar 16, 2022)
19-57398966-T-G		not specified	Uncertain significance (Dec 28, 2022)
19-57399026-C-T		not specified	Uncertain significance (Jan 27, 2022)
19-57399138-A-G		not specified	Likely benign (Oct 22, 2021)
19-57399174-T-G		not specified	Uncertain significance (Mar 31, 2023)
19-57399238-C-A		not specified	Uncertain significance (Aug 13, 2021)
19-57399312-G-C		not specified	Uncertain significance (Feb 17, 2022)
19-57399392-G-A		not specified	Uncertain significance (Jan 26, 2023)
19-57399414-A-G		not specified	Uncertain significance (Dec 02, 2022)
19-57399468-A-G		not specified	Uncertain significance (Dec 02, 2022)
19-57399560-G-A		not specified	Uncertain significance (Jan 26, 2022)
19-57399721-G-T		not specified	Uncertain significance (Aug 02, 2022)
19-57399788-G-A		not specified	Uncertain significance (Oct 06, 2022)
19-57399801-T-G		not specified	Uncertain significance (May 01, 2024)
19-57399854-A-G		not specified	Uncertain significance (Jan 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF548	protein_coding	protein_coding	ENST00000336128	4	11569

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.340	0.606	125724	0	5	125729	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.410	269	289	0.932	0.0000139	3648
Missense in Polyphen		72	85.421	0.84289		1079
Synonymous	1.09	89	103	0.864	0.00000536	938
Loss of Function	1.51	1	4.41	0.227	1.88e-7	50

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000581	0.0000581
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.00000881	0.00000879
Middle Eastern	0.000109	0.000109
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

• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.31

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.214
• ghis: 0.501

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.149

Gene Damage Prediction

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

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