ZNF677

zinc finger protein 677, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:53235380-53254898

Links

ENSG00000197928 ∙ NCBI:342926 ∙ ∙ HGNC:28730 ∙ Uniprot:Q86XU0 ∙ 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 ZNF677 gene.

• Inborn genetic diseases (27 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF677 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				2		2
missense			23	4		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	6	0

Variants in ZNF677

This is a list of pathogenic ClinVar variants found in the ZNF677 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-53237000-G-A		not specified	Likely benign (Sep 16, 2021)
19-53237009-T-C		not specified	Likely benign (Nov 22, 2022)
19-53237046-G-T		not specified	Uncertain significance (Jun 06, 2023)
19-53237055-G-C		not specified	Uncertain significance (Feb 07, 2023)
19-53237114-A-G		not specified	Likely benign (Sep 25, 2023)
19-53237198-G-A		not specified	Uncertain significance (Dec 28, 2022)
19-53237211-T-C		not specified	Uncertain significance (Feb 15, 2023)
19-53237219-G-A		not specified	Uncertain significance (Apr 08, 2022)
19-53237231-C-T		not specified	Uncertain significance (Feb 28, 2023)
19-53237520-A-G		not specified	Uncertain significance (Jul 30, 2023)
19-53237549-T-C		not specified	Uncertain significance (Aug 15, 2023)
19-53237562-T-C		not specified	Uncertain significance (Apr 13, 2023)
19-53237567-C-T		not specified	Uncertain significance (May 17, 2023)
19-53237592-C-G		not specified	Uncertain significance (Dec 17, 2023)
19-53237786-G-C		not specified	Uncertain significance (Sep 14, 2023)
19-53237794-T-A		not specified	Uncertain significance (Mar 20, 2023)
19-53237816-G-A		not specified	Uncertain significance (May 04, 2022)
19-53237939-T-A		not specified	Uncertain significance (Apr 25, 2023)
19-53237939-T-C		not specified	Uncertain significance (Jul 30, 2023)
19-53237955-T-C		not specified	Uncertain significance (May 25, 2022)
19-53238062-T-C		not specified	Uncertain significance (May 24, 2023)
19-53238066-T-C		not specified	Likely benign (Jul 06, 2021)
19-53238078-C-A		not specified	Uncertain significance (Sep 20, 2023)
19-53238170-C-T		not specified	Uncertain significance (Oct 12, 2021)
19-53238190-G-A			Likely benign (Feb 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF677	protein_coding	protein_coding	ENST00000333952	3	26575

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.66e-8	0.635	124698	5	1043	125746	0.00418

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0762	303	299	1.01	0.0000142	3927
Missense in Polyphen		65	76.209	0.85292		1005
Synonymous	-0.482	109	103	1.06	0.00000490	977
Loss of Function	1.21	15	21.0	0.714	8.76e-7	338

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00576	0.00570
Ashkenazi Jewish	0.00261	0.00248
East Asian	0.00181	0.00180
Finnish	0.00148	0.00148
European (Non-Finnish)	0.00641	0.00637
Middle Eastern	0.00181	0.00180
South Asian	0.00158	0.00154
Other	0.00459	0.00457

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Intolerance Scores

• loftool: 0.943
• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.6

Haploinsufficiency Scores

• pHI: 0.153
• hipred: N
• hipred_score: 0.112
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0955

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