ZNF397

zinc finger protein 397, the group of SCAN domain containing|Zinc fingers C2H2-type

Basic information

Region (hg38): 18:35241030-35267133

Previous symbols: [ "ZNF47" ]

Links

ENSG00000186812 ∙ NCBI:84307 ∙ OMIM:609601 ∙ HGNC:18818 ∙ Uniprot:Q8NF99 ∙ 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 ZNF397 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF397 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			1
missense			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			15			15
Total	0	0	34	1	0

Variants in ZNF397

This is a list of pathogenic ClinVar variants found in the ZNF397 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-35242508-C-A		not specified	Uncertain significance (Aug 11, 2021)
18-35242508-C-G		not specified	Uncertain significance (Jul 12, 2023)
18-35242561-T-A		not specified	Uncertain significance (Apr 26, 2023)
18-35242619-G-A		not specified	Uncertain significance (Feb 08, 2023)
18-35242669-G-C		not specified	Uncertain significance (Jun 04, 2024)
18-35242679-G-A		not specified	Likely benign (Sep 28, 2022)
18-35242822-G-A		not specified	Uncertain significance (May 08, 2024)
18-35243190-G-T		not specified	Uncertain significance (Nov 10, 2022)
18-35243285-C-T		not specified	Uncertain significance (Mar 31, 2024)
18-35245277-A-G		not specified	Uncertain significance (Sep 16, 2021)
18-35245325-C-T		not specified	Uncertain significance (Nov 03, 2022)
18-35245333-C-T		not specified	Uncertain significance (Nov 03, 2022)
18-35245343-G-C		not specified	Uncertain significance (Feb 27, 2023)
18-35245390-G-T		not specified	Uncertain significance (Sep 27, 2021)
18-35245410-A-C		not specified	Uncertain significance (Mar 25, 2024)
18-35245445-T-C		not specified	Uncertain significance (Jun 02, 2023)
18-35245513-A-G		not specified	Uncertain significance (Jul 06, 2021)
18-35245643-A-G		not specified	Uncertain significance (May 26, 2023)
18-35245676-T-G		not specified	Uncertain significance (Apr 08, 2024)
18-35245690-A-C		not specified	Uncertain significance (Jun 05, 2024)
18-35245742-G-A		not specified	Uncertain significance (Mar 20, 2024)
18-35245783-C-T		not specified	Uncertain significance (Jan 07, 2022)
18-35245840-A-G		not specified	Uncertain significance (Aug 28, 2023)
18-35246002-G-A		not specified	Uncertain significance (Aug 26, 2022)
18-35246165-G-A		not specified	Uncertain significance (Jun 11, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF397	protein_coding	protein_coding	ENST00000330501	3	26104

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000349	0.989	125717	0	31	125748	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	222	269	0.824	0.0000126	3503
Missense in Polyphen		74	102.87	0.71938		1307
Synonymous	0.634	87	94.9	0.917	0.00000445	947
Loss of Function	2.27	11	22.6	0.486	0.00000119	287

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000381	0.000381
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000548	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000962	0.0000879
Middle Eastern	0.0000548	0.0000544
South Asian	0.000232	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 3 acts as a DNA-dependent transcriptional repressor. {ECO:0000269|PubMed:12801647}.

Recessive Scores

• pRec: 0.0961

Intolerance Scores

• loftool: 0.876
• rvis_EVS: -0.29
• rvis_percentile_EVS: 32.94

Haploinsufficiency Scores

• pHI: 0.253
• hipred: N
• hipred_score: 0.172
• ghis: 0.629

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.960

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp397

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nucleolus;cytosol;plasma membrane;microtubule cytoskeleton
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;metal ion binding