ZBTB48

zinc finger and BTB domain containing 48, the group of Zinc fingers C2H2-type|BTB domain containing

Basic information

Region (hg38): 1:6579994-6589280

Previous symbols: [ "HKR3" ]

Links

ENSG00000204859 ∙ NCBI:3104 ∙ OMIM:165270 ∙ HGNC:4930 ∙ Uniprot:P10074 ∙ 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 ZBTB48 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZBTB48 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			25	2		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding						0
Total	0	0	25	3	0

Variants in ZBTB48

This is a list of pathogenic ClinVar variants found in the ZBTB48 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-6580768-C-A		not specified	Uncertain significance (Aug 11, 2022)
1-6580787-G-C		not specified	Uncertain significance (Jul 25, 2023)
1-6580982-G-C		not specified	Uncertain significance (Jan 26, 2022)
1-6581000-G-A		not specified	Uncertain significance (Sep 14, 2022)
1-6581005-C-T			Likely benign (Sep 01, 2022)
1-6581028-G-T		not specified	Uncertain significance (Mar 19, 2024)
1-6581043-C-T		not specified	Uncertain significance (Jan 17, 2023)
1-6581238-G-A		not specified	Uncertain significance (Jun 05, 2024)
1-6581288-G-A			Likely benign (Feb 01, 2023)
1-6582079-G-A		not specified	Uncertain significance (Aug 22, 2023)
1-6582158-C-T		not specified	Uncertain significance (Mar 19, 2024)
1-6582193-C-G		not specified	Uncertain significance (Mar 15, 2024)
1-6582202-G-A		not specified	Uncertain significance (Jun 07, 2023)
1-6585939-C-G		not specified	Uncertain significance (Jan 23, 2023)
1-6585950-C-T		not specified	Uncertain significance (Oct 27, 2022)
1-6585969-A-C		not specified	Uncertain significance (Aug 04, 2023)
1-6585975-G-C		not specified	Uncertain significance (Apr 18, 2023)
1-6586005-G-A		not specified	Uncertain significance (Jan 29, 2024)
1-6586702-C-T		not specified	Uncertain significance (Jul 12, 2023)
1-6586708-C-G		not specified	Uncertain significance (Aug 28, 2023)
1-6586777-T-C		not specified	Uncertain significance (Jun 22, 2023)
1-6587212-C-T		not specified	Uncertain significance (Oct 03, 2022)
1-6587612-G-A		not specified	Uncertain significance (Jan 23, 2024)
1-6587637-G-A			Likely benign (Feb 01, 2023)
1-6587639-G-A			Likely benign (May 08, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZBTB48	protein_coding	protein_coding	ENST00000377674	10	9280

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000115	0.999	125708	0	40	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	348	417	0.834	0.0000248	4526
Missense in Polyphen		123	169.95	0.72376		1751
Synonymous	-1.63	200	173	1.16	0.0000106	1351
Loss of Function	3.07	12	30.2	0.397	0.00000170	336

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000492	0.000491
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000116	0.000114
Middle Eastern	0.000218	0.000217
South Asian	0.000167	0.000163
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Telomere-binding protein that acts as a regulator of telomere length (PubMed:28500257, PubMed:28082411). Directly binds the telomeric double-stranded 5'-TTAGGG-3' repeat (PubMed:28500257, PubMed:28082411). Preferentially binds to telomeres that have a low concentration of shelterin complex and acts as a regulator of telomere length by initiating telomere trimming, a process that prevents the accumulation of aberrantly long telomeres (PubMed:28082411). Also acts as a transcription regulator that binds to promoter regions (PubMed:7969177, PubMed:24382891, PubMed:28500257). Regulates expression of a small subset of genes, including MTFP1 (PubMed:28500257). Regulates expression the J and/or S elements in MHC II promoter (PubMed:7969177). Acts as a negative regulator of cell proliferation by specifically activating expression of ARF, a tumor suppressor isoform of CDKN2A (PubMed:24382891). {ECO:0000269|PubMed:24382891, ECO:0000269|PubMed:28082411, ECO:0000269|PubMed:28500257, ECO:0000269|PubMed:7969177}.

Recessive Scores

• pRec: 0.155

Intolerance Scores

• loftool: 0.566
• rvis_EVS: -1
• rvis_percentile_EVS: 8.47

Haploinsufficiency Scores

• pHI: 0.129
• hipred: Y
• hipred_score: 0.532
• ghis: 0.592

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.866

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zbtb48

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;telomere maintenance via telomere lengthening;positive regulation of transcription, DNA-templated
• Cellular component: chromosome, telomeric region;nucleoplasm;cytosol
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;double-stranded telomeric DNA binding;DNA-binding transcription factor activity;protein binding;identical protein binding;transcription regulatory region DNA binding;metal ion binding