ZNF438

zinc finger protein 438, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 10:30820206-31031937

Links

ENSG00000183621 ∙ NCBI:220929 ∙ ∙ HGNC:21029 ∙ Uniprot:Q7Z4V0 ∙ 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 ZNF438 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF438 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				2		2
missense			50	7		57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	50	9	0

Variants in ZNF438

This is a list of pathogenic ClinVar variants found in the ZNF438 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-30844976-A-C		not specified	Uncertain significance (Feb 28, 2024)
10-30844980-G-C		not specified	Uncertain significance (May 15, 2023)
10-30844981-A-C		not specified	Uncertain significance (May 31, 2023)
10-30845006-G-A			Likely benign (Oct 01, 2022)
10-30845039-G-A			Likely benign (Oct 01, 2022)
10-30845081-C-G		not specified	Uncertain significance (Dec 08, 2023)
10-30845088-C-T		not specified	Likely benign (Aug 13, 2021)
10-30845089-G-A		not specified	Uncertain significance (Jul 06, 2022)
10-30845098-T-C		not specified	Uncertain significance (Mar 06, 2023)
10-30845137-A-G		not specified	Uncertain significance (Oct 10, 2023)
10-30845160-G-C		not specified	Uncertain significance (Apr 12, 2022)
10-30845175-T-G		not specified	Uncertain significance (Mar 01, 2024)
10-30845212-G-T		not specified	Uncertain significance (Sep 16, 2021)
10-30845215-C-T		not specified	Uncertain significance (Dec 08, 2023)
10-30845256-T-C		not specified	Uncertain significance (Apr 06, 2024)
10-30845284-C-T		not specified	Uncertain significance (Apr 11, 2023)
10-30845328-C-T		not specified	Uncertain significance (Apr 24, 2023)
10-30845350-C-T		not specified	Uncertain significance (Mar 16, 2024)
10-30845362-G-T		not specified	Uncertain significance (Oct 12, 2021)
10-30845364-T-A		not specified	Uncertain significance (May 30, 2024)
10-30845398-G-C		not specified	Uncertain significance (Oct 12, 2021)
10-30845565-T-C		not specified	Uncertain significance (Sep 15, 2021)
10-30848565-T-A		not specified	Uncertain significance (Feb 12, 2024)
10-30848609-G-A		not specified	Uncertain significance (Sep 22, 2023)
10-30848651-T-C		not specified	Uncertain significance (May 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF438	protein_coding	protein_coding	ENST00000436087	3	211731

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000267	0.766	125657	0	91	125748	0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.286	446	429	1.04	0.0000225	5450
Missense in Polyphen		106	103.8	1.0212		1370
Synonymous	-1.30	182	161	1.13	0.00000862	1645
Loss of Function	1.24	11	16.4	0.669	8.69e-7	243

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000466	0.000466
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000650	0.000647
European (Non-Finnish)	0.000256	0.000255
Middle Eastern	0.00	0.00
South Asian	0.000980	0.000948
Other	0.000662	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 1 acts as a transcriptional repressor.

Intolerance Scores

• loftool: 0.866
• rvis_EVS: 0.65
• rvis_percentile_EVS: 84.12

Haploinsufficiency Scores

• pHI: 0.0868
• hipred: N
• hipred_score: 0.123
• ghis: 0.448

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0431

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp438

Gene ontology

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