ZNF396

zinc finger protein 396, the group of Zinc fingers C2H2-type|SCAN domain containing

Basic information

Region (hg38): 18:35366694-35377337

Links

ENSG00000186496 ∙ NCBI:252884 ∙ OMIM:609600 ∙ HGNC:18824 ∙ Uniprot:Q96N95 ∙ 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 ZNF396 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF396 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			19	2		21
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	1

Variants in ZNF396

This is a list of pathogenic ClinVar variants found in the ZNF396 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-35369330-C-T		not specified	Uncertain significance (Feb 21, 2024)
18-35369336-T-C		not specified	Uncertain significance (Jun 26, 2024)
18-35369367-T-C		not specified	Uncertain significance (Sep 22, 2022)
18-35369370-C-A		not specified	Uncertain significance (Jun 30, 2022)
18-35369376-C-T		not specified	Likely benign (Nov 25, 2024)
18-35369460-C-T		not specified	Uncertain significance (Jan 08, 2024)
18-35369475-G-GT			Benign (Dec 31, 2019)
18-35369532-T-G		not specified	Uncertain significance (Sep 16, 2021)
18-35369590-A-C		not specified	Uncertain significance (Mar 20, 2024)
18-35369598-C-T		not specified	Uncertain significance (Jan 07, 2025)
18-35369600-A-G		not specified	Uncertain significance (Feb 06, 2023)
18-35369621-C-G		not specified	Uncertain significance (Aug 08, 2022)
18-35373581-T-C		not specified	Uncertain significance (Sep 13, 2023)
18-35373587-C-T		not specified	Likely benign (Jul 30, 2023)
18-35373591-C-T		not specified	Uncertain significance (Dec 21, 2022)
18-35374045-G-A		not specified	Uncertain significance (Dec 31, 2024)
18-35374079-G-A		not specified	Uncertain significance (Feb 16, 2023)
18-35374081-C-T		not specified	Uncertain significance (Apr 18, 2023)
18-35374118-C-T		not specified	Uncertain significance (Jul 19, 2022)
18-35374164-G-T		not specified	Uncertain significance (Nov 12, 2024)
18-35374171-T-G		not specified	Uncertain significance (Feb 27, 2023)
18-35374172-G-A		not specified	Uncertain significance (Dec 23, 2024)
18-35374205-C-T		not specified	Uncertain significance (Jun 19, 2024)
18-35374244-C-T		not specified	Uncertain significance (Oct 12, 2022)
18-35374255-G-A		not specified	Uncertain significance (Oct 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF396	protein_coding	protein_coding	ENST00000306346	4	10641

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000876	0.781	125345	6	397	125748	0.00160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.491	154	172	0.895	0.00000832	2183
Missense in Polyphen		23	28.966	0.79403		357
Synonymous	1.30	52	65.3	0.796	0.00000326	618
Loss of Function	1.23	10	15.2	0.659	7.46e-7	180

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0180	0.0179
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.00261	0.00261
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.00261	0.00261
South Asian	0.000919	0.000882
Other	0.00130	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 1 and isoform 2 act as DNA-dependent transcriptional repressors. {ECO:0000269|PubMed:12801647}.

Intolerance Scores

• loftool: 0.716
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.01

Haploinsufficiency Scores

• pHI: 0.0866
• hipred: N
• hipred_score: 0.112
• ghis: 0.521

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.920

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nucleus;cytoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding