ZNF780A

zinc finger protein 780A, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:40069151-40090943

Links

ENSG00000197782 ∙ NCBI:284323 ∙ ∙ HGNC:27603 ∙ Uniprot:O75290 ∙ 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 ZNF780A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF780A 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			46	2		48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	3	0

Variants in ZNF780A

This is a list of pathogenic ClinVar variants found in the ZNF780A region.

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

Position	Type	Phenotype	Significance	ClinVar
19-40074520-G-C		not specified	Uncertain significance (Mar 29, 2022)
19-40074543-G-T		not specified	Uncertain significance (May 03, 2023)
19-40074550-T-C		not specified	Uncertain significance (May 18, 2023)
19-40074553-C-T		not specified	Uncertain significance (Apr 04, 2023)
19-40074554-G-A		not specified	Uncertain significance (Dec 01, 2022)
19-40074623-G-C		not specified	Uncertain significance (Dec 19, 2023)
19-40074644-G-A		not specified	Uncertain significance (Jan 23, 2024)
19-40074676-T-C		not specified	Uncertain significance (Feb 14, 2024)
19-40074691-G-A		not specified	Uncertain significance (Apr 01, 2024)
19-40074759-T-C			Likely benign (Aug 01, 2023)
19-40074824-G-A		not specified	Uncertain significance (Dec 13, 2023)
19-40074892-G-C		not specified	Uncertain significance (Sep 14, 2022)
19-40074916-G-A		not specified	Uncertain significance (Feb 10, 2023)
19-40074931-T-C		not specified	Uncertain significance (Aug 08, 2022)
19-40074953-C-T		not specified	Uncertain significance (Apr 19, 2023)
19-40074965-T-G		not specified	Uncertain significance (Mar 29, 2022)
19-40074994-T-C		not specified	Uncertain significance (Feb 28, 2023)
19-40075048-C-T		not specified	Uncertain significance (Aug 30, 2022)
19-40075060-A-G		not specified	Uncertain significance (Jul 14, 2023)
19-40075060-A-T		not specified	Uncertain significance (Jun 07, 2024)
19-40075112-G-A		not specified	Uncertain significance (Aug 02, 2022)
19-40075161-A-C		not specified	Uncertain significance (Sep 20, 2023)
19-40075390-T-G		not specified	Uncertain significance (May 06, 2024)
19-40075393-C-T		not specified	Uncertain significance (Dec 19, 2022)
19-40075523-A-T		not specified	Uncertain significance (Jul 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF780A	protein_coding	protein_coding	ENST00000455521	4	21787

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000156	0.133	125741	0	5	125746	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.188	330	340	0.971	0.0000181	4317
Missense in Polyphen		100	111.84	0.89412		1537
Synonymous	-0.632	118	110	1.08	0.00000518	1116
Loss of Function	-0.564	8	6.45	1.24	2.72e-7	80

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation. {ECO:0000250}.

Intolerance Scores

• loftool: 0.896
• rvis_EVS: 1.13
• rvis_percentile_EVS: 92.29

Haploinsufficiency Scores

• pHI: 0.129
• hipred: N
• hipred_score: 0.112
• ghis: 0.477

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.171

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp607b

Gene ontology

• Biological process: regulation of transcription, DNA-templated
• Cellular component: nucleus
• Molecular function: DNA binding;metal ion binding