ZNF649

zinc finger protein 649, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:51889235-51905040

Links

ENSG00000198093 ∙ NCBI:65251 ∙ OMIM:611903 ∙ HGNC:25741 ∙ Uniprot:Q9BS31 ∙ 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 ZNF649 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF649 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			20	3		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	3	0

Variants in ZNF649

This is a list of pathogenic ClinVar variants found in the ZNF649 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-51890692-T-C		not specified	Uncertain significance (Jan 18, 2023)
19-51890709-C-T		not specified	Uncertain significance (May 23, 2023)
19-51890728-T-C		not specified	Likely benign (Jan 03, 2024)
19-51890742-T-C		not specified	Likely benign (Nov 03, 2023)
19-51890766-C-T		not specified	Uncertain significance (May 24, 2023)
19-51890803-G-A		not specified	Uncertain significance (Apr 04, 2024)
19-51890899-T-A		not specified	Uncertain significance (Dec 19, 2022)
19-51891115-T-C		not specified	Uncertain significance (Oct 30, 2023)
19-51891159-C-G		not specified	Uncertain significance (Aug 15, 2023)
19-51891207-C-T		not specified	Uncertain significance (Jul 25, 2023)
19-51891256-C-T		not specified	Uncertain significance (Mar 29, 2022)
19-51891276-A-T		not specified	Likely benign (Aug 26, 2022)
19-51891291-C-T		not specified	Uncertain significance (Dec 05, 2022)
19-51891381-T-C		not specified	Uncertain significance (Dec 03, 2021)
19-51891463-C-T		not specified	Uncertain significance (Feb 28, 2023)
19-51891517-C-G		not specified	Uncertain significance (Mar 31, 2023)
19-51891553-C-T		not specified	Uncertain significance (Jan 30, 2024)
19-51891604-G-C		not specified	Uncertain significance (Mar 14, 2023)
19-51891616-T-G		not specified	Uncertain significance (Feb 11, 2022)
19-51891689-T-G		not specified	Uncertain significance (Jun 11, 2024)
19-51891804-A-G		not specified	Uncertain significance (May 18, 2023)
19-51891817-G-T		not specified	Uncertain significance (Dec 30, 2023)
19-51896499-C-T		not specified	Uncertain significance (Mar 06, 2023)
19-51896525-T-G		not specified	Uncertain significance (Feb 07, 2023)
19-51900098-C-A		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF649	protein_coding	protein_coding	ENST00000354957	4	15817

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0737	0.878	125727	0	19	125746	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.41	200	265	0.756	0.0000133	3341
Missense in Polyphen		39	74.977	0.52016		1004
Synonymous	-0.255	102	98.8	1.03	0.00000558	912
Loss of Function	1.67	3	8.16	0.368	4.29e-7	91

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000260	0.000260
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000703	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor. Regulator of transcriptional factor complexes and may suppress SRE and AP-1 transcription activities mediated by growth factor signaling pathways. {ECO:0000269|PubMed:15950191}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Intolerance Scores

• loftool: 0.368
• rvis_EVS: 0.75
• rvis_percentile_EVS: 86.71

Haploinsufficiency Scores

• pHI: 0.385
• hipred: N
• hipred_score: 0.252
• ghis: 0.428

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.191

Gene Damage Prediction

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

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;positive regulation of transcription by RNA polymerase II
• Cellular component: extracellular space;nucleus;nucleoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;transcription regulatory region DNA binding;metal ion binding