ZNF678

zinc finger protein 678, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 1:227563543-227677443

Links

ENSG00000181450 ∙ NCBI:339500 ∙ ∙ HGNC:28652 ∙ Uniprot:Q5SXM1 ∙ 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 ZNF678 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF678 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			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			2			2
Total	0	0	29	0	0

Variants in ZNF678

This is a list of pathogenic ClinVar variants found in the ZNF678 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-227646544-G-A		not specified	Uncertain significance (Mar 02, 2023)
1-227646572-T-C		not specified	Uncertain significance (Oct 02, 2023)
1-227646667-C-A		not specified	Uncertain significance (Oct 06, 2022)
1-227654338-A-G		not specified	Uncertain significance (Feb 16, 2023)
1-227654420-G-A		not specified	Uncertain significance (Jun 21, 2023)
1-227654531-G-A		not specified	Uncertain significance (Nov 17, 2023)
1-227654555-G-A		not specified	Uncertain significance (Jan 04, 2024)
1-227654627-A-T		not specified	Uncertain significance (May 05, 2023)
1-227654719-G-A		not specified	Uncertain significance (Sep 12, 2023)
1-227654755-A-G		not specified	Uncertain significance (May 13, 2024)
1-227654829-G-T		not specified	Uncertain significance (Nov 29, 2021)
1-227654846-A-G		not specified	Uncertain significance (Sep 15, 2021)
1-227654888-A-G		not specified	Uncertain significance (Oct 26, 2022)
1-227654936-G-T		not specified	Uncertain significance (Sep 16, 2021)
1-227654948-G-T		not specified	Uncertain significance (May 17, 2023)
1-227655004-C-T		not specified	Uncertain significance (Jan 20, 2023)
1-227655014-A-G		not specified	Uncertain significance (Jan 26, 2022)
1-227655098-A-G		not specified	Uncertain significance (Sep 12, 2023)
1-227655125-C-G		not specified	Uncertain significance (Jan 10, 2022)
1-227655181-C-T		not specified	Uncertain significance (Dec 14, 2023)
1-227655253-C-T		not specified	Uncertain significance (Dec 28, 2023)
1-227655293-C-A		not specified	Uncertain significance (Feb 16, 2023)
1-227655325-A-G		not specified	Uncertain significance (Sep 28, 2022)
1-227655338-A-G		not specified	Uncertain significance (Feb 12, 2024)
1-227655460-C-A		not specified	Uncertain significance (Nov 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF678	protein_coding	protein_coding	ENST00000343776	2	113901

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0159	0.481	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.691	294	263	1.12	0.0000122	3461
Missense in Polyphen		75	65.713	1.1413		938
Synonymous	-1.43	105	87.9	1.19	0.00000401	872
Loss of Function	-0.620	2	1.25	1.60	5.28e-8	16

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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)

Haploinsufficiency Scores

• pHI: 0.196
• hipred: N
• hipred_score: 0.148
• ghis: 0.509

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0741

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;metal ion binding