ZNF544

zinc finger protein 544, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:58228593-58277495

Links

ENSG00000198131 ∙ NCBI:27300 ∙ ∙ HGNC:16759 ∙ Uniprot:Q6NX49 ∙ 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 ZNF544 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF544 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				2		2
missense			55	5		60
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	55	7	1

Variants in ZNF544

This is a list of pathogenic ClinVar variants found in the ZNF544 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-58244034-G-A		not specified	Uncertain significance (Jan 06, 2023)
19-58244040-T-C		not specified	Uncertain significance (Nov 29, 2023)
19-58244049-C-T		not specified	Uncertain significance (Jun 22, 2023)
19-58246315-C-T			Likely benign (Feb 01, 2023)
19-58246367-G-C		not specified	Uncertain significance (Aug 17, 2022)
19-58246368-C-T		not specified	Uncertain significance (Sep 07, 2022)
19-58246711-G-T		not specified	Uncertain significance (Feb 27, 2024)
19-58246791-C-G		not specified	Uncertain significance (Oct 12, 2022)
19-58246792-G-A		not specified	Uncertain significance (Oct 05, 2023)
19-58260874-A-C		not specified	Uncertain significance (Oct 21, 2021)
19-58260899-G-A		not specified	Uncertain significance (Apr 26, 2023)
19-58260939-G-C		not specified	Uncertain significance (Jun 17, 2024)
19-58260964-T-A		not specified	Uncertain significance (Mar 03, 2022)
19-58260984-A-C		not specified	Likely benign (Sep 07, 2022)
19-58261078-G-A		not specified	Uncertain significance (Jul 14, 2021)
19-58261090-G-T		not specified	Uncertain significance (Mar 14, 2023)
19-58261118-T-C		not specified	Uncertain significance (Dec 11, 2023)
19-58261154-G-A		not specified	Uncertain significance (Jun 09, 2022)
19-58261184-A-G		not specified	Uncertain significance (Jan 23, 2023)
19-58261194-A-T		not specified	Uncertain significance (May 01, 2024)
19-58261250-G-A		not specified	Likely benign (Mar 07, 2024)
19-58261255-C-A		not specified	Uncertain significance (Jun 17, 2024)
19-58261261-G-A		not specified	Uncertain significance (Dec 15, 2023)
19-58261282-A-G		not specified	Uncertain significance (Mar 06, 2023)
19-58261306-G-A		not specified	Likely benign (May 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF544	protein_coding	protein_coding	ENST00000269829	4	48856

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000995	0.607	125713	0	23	125736	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.716	412	373	1.10	0.0000185	4726
Missense in Polyphen		132	120.22	1.098		1516
Synonymous	-0.396	144	138	1.04	0.00000720	1300
Loss of Function	0.529	5	6.45	0.775	3.63e-7	58

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000369	0.000369
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.0000705	0.0000703
Middle Eastern	0.000326	0.000326
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: 0.938
• rvis_EVS: 0.63
• rvis_percentile_EVS: 83.57

Haploinsufficiency Scores

• pHI: 0.641
• hipred: N
• hipred_score: 0.112
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.199

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;protein binding;metal ion binding