ZNF609

zinc finger protein 609, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 15:64460578-64686068

Links

ENSG00000180357 ∙ NCBI:23060 ∙ OMIM:617474 ∙ HGNC:29003 ∙ Uniprot:O15014 ∙ 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 ZNF609 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF609 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	3	4
missense			76	1	1	78
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	76	2	4

Variants in ZNF609

This is a list of pathogenic ClinVar variants found in the ZNF609 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-64499465-A-C		not specified	Uncertain significance (Jul 27, 2022)
15-64499467-C-G		not specified	Uncertain significance (Mar 31, 2024)
15-64499481-A-G		not specified	Uncertain significance (Jan 31, 2022)
15-64499540-G-A		not specified	Uncertain significance (Aug 30, 2022)
15-64499693-A-G		not specified	Uncertain significance (Jun 24, 2022)
15-64499697-G-A		not specified	Likely benign (Jun 18, 2021)
15-64499754-G-C		not specified	Uncertain significance (Aug 30, 2022)
15-64499808-A-G		not specified	Uncertain significance (Jun 01, 2023)
15-64499843-G-T			Benign (May 10, 2018)
15-64499856-C-T		not specified	Uncertain significance (Jul 14, 2021)
15-64499882-G-A		not specified	Uncertain significance (Jan 23, 2024)
15-64500134-T-C		not specified	Uncertain significance (Sep 14, 2022)
15-64500137-C-T		not specified	Uncertain significance (Nov 09, 2021)
15-64500159-C-T		not specified	Uncertain significance (Mar 01, 2024)
15-64622846-C-T		not specified	Uncertain significance (Sep 29, 2023)
15-64622874-G-T		not specified	Uncertain significance (May 21, 2024)
15-64622888-A-T		not specified	Uncertain significance (Feb 21, 2024)
15-64622939-T-C		not specified	Uncertain significance (Aug 25, 2021)
15-64622947-A-G		not specified	Uncertain significance (Sep 14, 2022)
15-64673974-C-T		not specified	Uncertain significance (Apr 15, 2024)
15-64674116-C-T		not specified	Uncertain significance (Apr 14, 2022)
15-64674118-C-A		not specified	Uncertain significance (Jan 03, 2024)
15-64674146-A-G		not specified	Uncertain significance (Feb 28, 2023)
15-64674196-A-G		not specified	Uncertain significance (Dec 20, 2023)
15-64674331-G-A		not specified	Uncertain significance (May 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF609	protein_coding	protein_coding	ENST00000326648	8	225324

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000168	125739	0	5	125744	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.83	651	796	0.818	0.0000450	9203
Missense in Polyphen		248	326.56	0.75944		3750
Synonymous	-0.289	310	304	1.02	0.0000169	2851
Loss of Function	6.18	3	50.3	0.0596	0.00000289	639

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor, which activates RAG1, and possibly RAG2, transcription. Through the regulation of RAG1/2 expression, may regulate thymocyte maturation. Along with NIPBL and the multiprotein complex Integrator, promotes cortical neuron migration during brain development by regulating the transcription of crucial genes in this process. Preferentially binds promoters containing paused RNA polymerase II. Up-regulates the expression of SEMA3A, NRP1, PLXND1 and GABBR2 genes, among others. {ECO:0000250|UniProtKB:Q8BZ47}.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.00751
• rvis_EVS: -2.58
• rvis_percentile_EVS: 0.83

Haploinsufficiency Scores

• pHI: 0.936
• hipred: Y
• hipred_score: 0.591
• ghis: 0.629

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.309

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp609
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;muscle organ development;positive regulation of transcription by RNA polymerase II;regulation of myoblast proliferation;positive regulation of neuron migration
• Cellular component: nucleus;nucleoplasm;integrator complex
• Molecular function: nucleic acid binding;metal ion binding