ZNF839

zinc finger protein 839

Basic information

Region (hg38): 14:102317377-102342702

Previous symbols: [ "C14orf131" ]

Links

ENSG00000022976 ∙ NCBI:55778 ∙ ∙ HGNC:20345 ∙ Uniprot:A8K0R7 ∙ 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 ZNF839 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF839 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				4		4
missense			60	11	1	72
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	60	15	1

Variants in ZNF839

This is a list of pathogenic ClinVar variants found in the ZNF839 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-102319770-C-G		not specified	Uncertain significance (Oct 02, 2023)
14-102319771-G-T			Likely benign (Jul 01, 2022)
14-102319796-G-C		not specified	Uncertain significance (Oct 05, 2023)
14-102319809-G-A		not specified	Uncertain significance (Feb 01, 2023)
14-102319814-G-A		not specified	Uncertain significance (May 29, 2024)
14-102319820-G-T		not specified	Uncertain significance (Dec 20, 2022)
14-102319827-C-G		not specified	Uncertain significance (Sep 29, 2023)
14-102319848-G-T		not specified	Uncertain significance (Nov 30, 2021)
14-102319852-C-A		not specified	Uncertain significance (Jan 26, 2022)
14-102319860-G-T		not specified	Uncertain significance (Apr 04, 2024)
14-102319883-C-A		not specified	Uncertain significance (Feb 28, 2023)
14-102319901-G-C		not specified	Uncertain significance (Jan 19, 2024)
14-102319937-C-T		not specified	Uncertain significance (Dec 07, 2021)
14-102319941-C-A		not specified	Uncertain significance (Jun 09, 2022)
14-102319941-C-G		not specified	Uncertain significance (Jun 18, 2024)
14-102319950-T-A		not specified	Uncertain significance (Dec 07, 2021)
14-102319956-A-G		not specified	Uncertain significance (Dec 07, 2021)
14-102319971-T-G		not specified	Uncertain significance (Feb 09, 2022)
14-102319977-A-G		not specified	Uncertain significance (Jul 06, 2021)
14-102319986-A-C		not specified	Uncertain significance (Oct 12, 2021)
14-102320049-C-T		not specified	Uncertain significance (Oct 27, 2022)
14-102326204-T-C		not specified	Likely benign (Dec 08, 2023)
14-102326258-G-A		not specified	Uncertain significance (Apr 29, 2024)
14-102326349-C-T		not specified	Uncertain significance (Oct 17, 2023)
14-102326401-A-C		not specified	Uncertain significance (May 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF839	protein_coding	protein_coding	ENST00000442396	8	25331

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000382	0.990	124601	1	37	124639	0.000152

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.921	420	477	0.881	0.0000270	5874
Missense in Polyphen		91	135.14	0.67336		1748
Synonymous	-0.468	209	201	1.04	0.0000122	2005
Loss of Function	2.30	11	22.9	0.481	0.00000129	300

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.000101	0.0000994
East Asian	0.000167	0.000167
Finnish	0.00	0.00
European (Non-Finnish)	0.000205	0.000195
Middle Eastern	0.000167	0.000167
South Asian	0.000266	0.000261
Other	0.000167	0.000165

dbNSFP

Source: dbNSFP

• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Intolerance Scores

• loftool: 0.897
• rvis_EVS: 1.5
• rvis_percentile_EVS: 95.38

Haploinsufficiency Scores

• pHI: 0.0931
• hipred: N
• hipred_score: 0.145
• ghis: 0.396

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.475

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp839

Gene ontology

• Molecular function: nucleic acid binding;metal ion binding