ZNF280D

zinc finger protein 280D, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 15:56630176-56734086

Previous symbols: [ "SUHW4" ]

Links

ENSG00000137871 ∙ NCBI:54816 ∙ ∙ HGNC:25953 ∙ Uniprot:Q6N043 ∙ 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 ZNF280D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF280D 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			43	2		45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	43	2	0

Variants in ZNF280D

This is a list of pathogenic ClinVar variants found in the ZNF280D region.

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

Position	Type	Phenotype	Significance	ClinVar
15-56631502-C-T		not specified	Uncertain significance (Dec 19, 2022)
15-56631589-A-G		not specified	Uncertain significance (May 17, 2023)
15-56631756-A-T		not specified	Uncertain significance (Mar 19, 2024)
15-56631763-C-T		not specified	Uncertain significance (May 06, 2022)
15-56631769-T-C		not specified	Uncertain significance (Jun 19, 2024)
15-56631791-C-G		not specified	Uncertain significance (Jan 05, 2022)
15-56631795-A-C		not specified	Uncertain significance (May 15, 2024)
15-56631998-G-C		not specified	Uncertain significance (Sep 26, 2022)
15-56632021-G-A		not specified	Uncertain significance (Nov 03, 2022)
15-56632122-A-G		not specified	Likely benign (Oct 05, 2023)
15-56654220-G-A		not specified	Uncertain significance (Dec 08, 2023)
15-56654221-G-C		not specified	Uncertain significance (Jan 03, 2024)
15-56654417-T-C		not specified	Uncertain significance (Mar 19, 2024)
15-56654477-C-T		not specified	Uncertain significance (Aug 14, 2023)
15-56658442-T-C		not specified	Uncertain significance (Jul 20, 2022)
15-56666428-C-T		not specified	Uncertain significance (Mar 04, 2024)
15-56666464-G-A		not specified	Uncertain significance (Oct 27, 2022)
15-56666497-G-T		not specified	Uncertain significance (Feb 27, 2024)
15-56666509-A-G		not specified	Uncertain significance (Sep 16, 2021)
15-56666528-G-A		not specified	Uncertain significance (May 17, 2023)
15-56666712-T-C		not specified	Uncertain significance (Sep 29, 2023)
15-56666833-T-C		not specified	Uncertain significance (Jun 17, 2024)
15-56666892-G-T		not specified	Uncertain significance (Nov 04, 2022)
15-56666908-G-A		not specified	Uncertain significance (Jul 19, 2023)
15-56666929-T-C		not specified	Uncertain significance (Mar 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF280D	protein_coding	protein_coding	ENST00000267807	20	288391

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0468	0.953	125728	0	11	125739	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.18	414	487	0.850	0.0000234	6503
Missense in Polyphen		62	111.33	0.55689		1541
Synonymous	-1.33	189	167	1.13	0.00000861	1725
Loss of Function	4.68	12	46.4	0.259	0.00000233	661

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000190	0.000186
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000371	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as a transcription factor.

Intolerance Scores

• loftool: 0.672
• rvis_EVS: -0.77
• rvis_percentile_EVS: 13.1

Haploinsufficiency Scores

• pHI: 0.427
• hipred: N
• hipred_score: 0.346
• ghis: 0.615

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.485

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp280d

Gene ontology

• Biological process: regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;nucleic acid binding;DNA binding;DNA-binding transcription factor activity;metal ion binding