ZNF398

zinc finger protein 398, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 7:149126415-149183042

Links

ENSG00000197024 ∙ ∙ OMIM:618593 ∙ HGNC:18373 ∙ Uniprot:Q8TD17 ∙ 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 ZNF398 gene.

• Inborn genetic diseases (28 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF398 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			25	2		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	26	2	0

Variants in ZNF398

This is a list of pathogenic ClinVar variants found in the ZNF398 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-149154080-G-C		not specified	Uncertain significance (Oct 06, 2021)
7-149154194-C-A		not specified	Uncertain significance (May 17, 2023)
7-149154239-G-A		not specified	Uncertain significance (Jan 08, 2024)
7-149154311-C-T		not specified	Uncertain significance (Jan 18, 2023)
7-149166264-A-G		not specified	Uncertain significance (May 25, 2022)
7-149166825-A-G		not specified	Uncertain significance (Mar 25, 2022)
7-149176527-G-A		not specified	Uncertain significance (Feb 08, 2023)
7-149176552-A-C		not specified	Uncertain significance (Aug 02, 2021)
7-149176570-G-A		not specified	Uncertain significance (Feb 17, 2022)
7-149178659-G-A		not specified	Uncertain significance (Sep 27, 2022)
7-149178673-A-T		not specified	Uncertain significance (Nov 29, 2021)
7-149178690-C-T		not specified	Uncertain significance (Jul 11, 2023)
7-149178782-A-G		not specified	Likely benign (Dec 21, 2022)
7-149178786-C-T		not specified	Uncertain significance (May 24, 2023)
7-149178837-G-A		not specified	Uncertain significance (Jul 11, 2023)
7-149178878-C-A		not specified	Uncertain significance (Jan 26, 2023)
7-149178903-C-T		not specified	Uncertain significance (Jul 14, 2022)
7-149178983-C-T		not specified	Uncertain significance (Nov 21, 2022)
7-149179046-C-T		not specified	Uncertain significance (Mar 29, 2022)
7-149179065-C-T		not specified	Uncertain significance (Sep 07, 2022)
7-149179100-C-T		not specified	Uncertain significance (Dec 30, 2023)
7-149179113-C-T		not specified	Uncertain significance (Feb 17, 2023)
7-149179194-G-A		not specified	Uncertain significance (May 13, 2022)
7-149179238-C-T		not specified	Uncertain significance (Jun 03, 2022)
7-149179295-C-T		not specified	Uncertain significance (Sep 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF398	protein_coding	protein_coding	ENST00000475153	6	56609

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.146	0.854	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	314	372	0.844	0.0000222	4203
Missense in Polyphen		128	175.3	0.73019		1881
Synonymous	0.912	128	142	0.903	0.00000780	1305
Loss of Function	3.32	6	23.3	0.258	0.00000115	268

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Function as a transcriptional activator.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.282
• rvis_EVS: -0.57
• rvis_percentile_EVS: 18.9

Haploinsufficiency Scores

• pHI: 0.496
• hipred: N
• hipred_score: 0.436
• ghis: 0.587

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.987

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp398

Gene ontology

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