ZNF646

zinc finger protein 646, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 16:31074421-31084196

Links

ENSG00000167395 ∙ NCBI:9726 ∙ OMIM:619299 ∙ HGNC:29004 ∙ Uniprot:O15015 ∙ 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 ZNF646 gene.

• Inborn genetic diseases (100 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF646 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			93	6		99
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	96	8	0

Variants in ZNF646

This is a list of pathogenic ClinVar variants found in the ZNF646 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-31076367-C-T		not specified	Uncertain significance (Sep 14, 2022)
16-31076368-G-A		not specified	Uncertain significance (Oct 27, 2022)
16-31076398-G-A		not specified	Uncertain significance (Dec 28, 2022)
16-31076431-A-G		not specified	Uncertain significance (Dec 20, 2021)
16-31076436-A-G		not specified	Uncertain significance (Jun 01, 2023)
16-31076524-G-T		not specified	Uncertain significance (Sep 14, 2022)
16-31076578-C-G		not specified	Uncertain significance (May 17, 2023)
16-31076619-C-T		not specified	Uncertain significance (Jul 06, 2021)
16-31076631-C-T		not specified	Uncertain significance (Aug 08, 2023)
16-31076644-C-T		not specified	Uncertain significance (Dec 14, 2023)
16-31076656-A-G		not specified	Uncertain significance (Apr 12, 2022)
16-31076686-C-T		not specified	Uncertain significance (Jan 17, 2024)
16-31076748-A-G		not specified	Uncertain significance (Jan 17, 2024)
16-31076755-C-A		not specified	Uncertain significance (Apr 13, 2022)
16-31076895-A-G		not specified	Uncertain significance (Aug 30, 2021)
16-31077012-T-G		not specified	Uncertain significance (Jun 27, 2022)
16-31077213-C-G		not specified	Uncertain significance (Jun 27, 2022)
16-31077225-C-T		not specified	Uncertain significance (Mar 24, 2023)
16-31077343-G-C		not specified	Uncertain significance (Nov 09, 2023)
16-31077374-G-A		not specified	Uncertain significance (Sep 27, 2021)
16-31077394-T-G		not specified	Uncertain significance (Jun 28, 2022)
16-31077438-C-T		not specified	Uncertain significance (Mar 01, 2024)
16-31077447-C-T		not specified	Uncertain significance (Jan 05, 2022)
16-31077606-C-A		not specified	Uncertain significance (Jan 19, 2024)
16-31077610-G-C		not specified	Uncertain significance (Apr 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF646	protein_coding	protein_coding	ENST00000300850	2	9775

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000678	1.00	125689	0	59	125748	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.638	1080	1.14e+3	0.947	0.0000724	11951
Missense in Polyphen		381	447.35	0.85168		4628
Synonymous	-0.683	454	436	1.04	0.0000243	3789
Loss of Function	4.37	19	53.5	0.355	0.00000320	590

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000395	0.000304
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.000328	0.000326
Finnish	0.000187	0.000185
European (Non-Finnish)	0.000277	0.000273
Middle Eastern	0.000328	0.000326
South Asian	0.000327	0.000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.

Recessive Scores

• pRec: 0.0960

Intolerance Scores

• loftool: 0.534
• rvis_EVS: 0.23
• rvis_percentile_EVS: 68.55

Haploinsufficiency Scores

• pHI: 0.265
• hipred: N
• hipred_score: 0.270
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.966

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Zfp646

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;DNA binding;DNA-binding transcription factor activity;protein binding;metal ion binding