ZNF48

zinc finger protein 48, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 16:30378106-30400108

Previous symbols: [ "ZNF553" ]

Links

ENSG00000180035 ∙ NCBI:197407 ∙ ∙ HGNC:13114 ∙ Uniprot:Q96MX3 ∙ 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 ZNF48 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF48 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			40			40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	0	0

Variants in ZNF48

This is a list of pathogenic ClinVar variants found in the ZNF48 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-30395814-C-G		not specified	Uncertain significance (May 17, 2023)
16-30395840-G-C		not specified	Uncertain significance (Jun 21, 2022)
16-30395843-G-A		not specified	Uncertain significance (Mar 16, 2024)
16-30395847-G-C		not specified	Uncertain significance (Oct 14, 2023)
16-30397356-C-G		not specified	Uncertain significance (Jul 27, 2021)
16-30397434-G-A		not specified	Uncertain significance (Aug 30, 2021)
16-30397470-A-C		not specified	Uncertain significance (May 23, 2023)
16-30397485-T-C		not specified	Uncertain significance (Nov 23, 2021)
16-30397521-C-T		not specified	Uncertain significance (Jun 07, 2024)
16-30397536-C-T		not specified	Uncertain significance (Jan 23, 2023)
16-30397537-G-A		not specified	Uncertain significance (Feb 06, 2023)
16-30397546-G-A		not specified	Uncertain significance (Jun 07, 2024)
16-30397551-C-A		not specified	Uncertain significance (Jan 20, 2023)
16-30397579-G-A		not specified	Uncertain significance (Jan 23, 2023)
16-30397644-C-T		not specified	Uncertain significance (Aug 30, 2022)
16-30397741-G-A		not specified	Uncertain significance (May 29, 2024)
16-30397761-C-T		not specified	Uncertain significance (Jun 11, 2024)
16-30397762-G-A		not specified	Uncertain significance (Dec 01, 2022)
16-30397768-C-A		not specified	Uncertain significance (Oct 20, 2021)
16-30397801-G-A		not specified	Uncertain significance (Apr 30, 2024)
16-30397813-G-C		not specified	Uncertain significance (Sep 16, 2021)
16-30397978-G-C		not specified	Uncertain significance (Jan 08, 2024)
16-30397978-G-T		not specified	Uncertain significance (Aug 12, 2021)
16-30397996-G-A		not specified	Uncertain significance (May 23, 2023)
16-30398007-C-T		not specified	Uncertain significance (Jun 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF48	protein_coding	protein_coding	ENST00000320159	2	22003

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00668	0.990	125722	0	24	125746	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.27	333	405	0.822	0.0000265	3977
Missense in Polyphen		105	157.27	0.66763		1530
Synonymous	0.720	143	154	0.926	0.00000885	1317
Loss of Function	2.56	7	19.1	0.367	0.00000137	189

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000163	0.000163
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.000163	0.000163
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• loftool: 0.667
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.73

Haploinsufficiency Scores

• pHI: 0.192
• hipred: Y
• hipred_score: 0.627
• ghis: 0.537

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0308

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp553
• 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
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding