ZNF169

zinc finger protein 169, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 9:94259298-94303967

Links

ENSG00000175787 ∙ NCBI:169841 ∙ OMIM:603404 ∙ HGNC:12957 ∙ Uniprot:Q14929 ∙ 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 ZNF169 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF169 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			45	2		47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	2	0

Variants in ZNF169

This is a list of pathogenic ClinVar variants found in the ZNF169 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-94292357-G-A		not specified	Uncertain significance (Dec 03, 2021)
9-94292376-C-G		not specified	Uncertain significance (Aug 27, 2024)
9-94293003-G-A		not specified	Uncertain significance (Aug 02, 2021)
9-94293017-A-C		not specified	Uncertain significance (Aug 20, 2024)
9-94299815-A-G		not specified	Uncertain significance (Mar 31, 2022)
9-94299857-C-T		not specified	Uncertain significance (Nov 30, 2021)
9-94299865-A-C		not specified	Uncertain significance (May 31, 2023)
9-94299889-G-C		not specified	Uncertain significance (Dec 11, 2023)
9-94300044-G-C		not specified	Uncertain significance (May 13, 2024)
9-94300103-G-A		not specified	Uncertain significance (Jan 05, 2022)
9-94300142-G-T		not specified	Uncertain significance (Sep 01, 2021)
9-94300150-G-T		not specified	Uncertain significance (Jan 16, 2025)
9-94300156-A-G		not specified	Uncertain significance (Jun 28, 2024)
9-94300159-T-G		not specified	Uncertain significance (May 24, 2023)
9-94300196-T-C		not specified	Uncertain significance (May 25, 2022)
9-94300198-C-T		not specified	Likely benign (Oct 19, 2024)
9-94300208-A-G		not specified	Uncertain significance (Mar 09, 2025)
9-94300236-C-G		not specified	Uncertain significance (Mar 18, 2024)
9-94300276-G-A		not specified	Uncertain significance (Mar 06, 2023)
9-94300312-C-T		not specified	Uncertain significance (Apr 21, 2022)
9-94300330-G-A		not specified	Uncertain significance (Feb 17, 2022)
9-94300340-C-T		not specified	Uncertain significance (Oct 26, 2021)
9-94300360-G-T		not specified	Uncertain significance (Jul 27, 2024)
9-94300364-G-A		not specified	Uncertain significance (Dec 02, 2024)
9-94300381-G-T		not specified	Likely benign (Nov 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF169	protein_coding	protein_coding	ENST00000395395	4	42144

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.60e-12	0.0819	125605	0	143	125748	0.000569

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.216	331	342	0.967	0.0000188	3941
Missense in Polyphen		103	113.69	0.90596		1309
Synonymous	-0.812	148	136	1.09	0.00000758	1189
Loss of Function	0.370	18	19.8	0.910	0.00000101	243

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00269	0.00269
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000816	0.000816
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000529	0.000528
Middle Eastern	0.000816	0.000816
South Asian	0.000492	0.000490
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.911
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.47

Haploinsufficiency Scores

• pHI: 0.155
• hipred: N
• hipred_score: 0.112
• ghis: 0.507

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.292

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp169

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;protein binding;metal ion binding