ZFAT

zinc finger and AT-hook domain containing, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 8:134477787-134713049

Previous symbols: [ "ZNF406", "ZFAT1" ]

Links

ENSG00000066827 ∙ NCBI:57623 ∙ OMIM:610931 ∙ HGNC:19899 ∙ Uniprot:Q9P243 ∙ 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 ZFAT gene.

• Inborn genetic diseases (50 variants)
• not provided (11 variants)
• not specified (1 variants)
• Autoimmune thyroid disease, susceptibility to, 3 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZFAT 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	4	5
missense			49	3	4	56
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	49	4	8

Variants in ZFAT

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

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

Position	Type	Phenotype	Significance	ClinVar
8-134478531-A-G		not specified	Uncertain significance (Apr 26, 2023)
8-134478532-T-A		not specified	Uncertain significance (Dec 15, 2022)
8-134478561-G-A		Autoimmune thyroid disease, susceptibility to, 3	Uncertain significance (May 14, 2020)
8-134478594-G-A		not specified	Uncertain significance (Jun 06, 2023)
8-134478659-C-T			Benign/Likely benign (May 01, 2022)
8-134478672-G-A		not specified	Uncertain significance (Oct 12, 2021)
8-134478681-A-G		not specified	Uncertain significance (Feb 06, 2023)
8-134478707-C-G		not specified	Uncertain significance (Jun 24, 2022)
8-134478708-T-G		not specified	Uncertain significance (Nov 22, 2023)
8-134509637-C-T			Benign (Dec 31, 2019)
8-134509638-G-A		not specified	Uncertain significance (Dec 05, 2022)
8-134509731-G-A		not specified	Uncertain significance (Jan 23, 2023)
8-134509746-T-C		not specified	Uncertain significance (May 30, 2023)
8-134509747-C-T		not specified	Uncertain significance (Jun 29, 2022)
8-134512507-G-A		not specified	Uncertain significance (Sep 30, 2021)
8-134512583-C-T		not specified	Uncertain significance (Feb 22, 2023)
8-134520899-C-T		not specified	Uncertain significance (Jan 19, 2022)
8-134520970-T-C			Benign (Dec 31, 2019)
8-134520990-A-T		not specified	Uncertain significance (Nov 08, 2022)
8-134532867-C-T		not specified	Uncertain significance (Jun 29, 2023)
8-134532869-G-C		not specified	Likely benign (Apr 21, 2022)
8-134532909-T-G		not specified	Uncertain significance (Feb 26, 2024)
8-134532950-T-C		not specified	Uncertain significance (Mar 20, 2023)
8-134532966-G-A		not specified	Uncertain significance (Dec 19, 2023)
8-134565373-G-A		not specified	Uncertain significance (Sep 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZFAT	protein_coding	protein_coding	ENST00000377838	16	235262

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.28e-8	1.00	124762	0	44	124806	0.000176

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.60	602	723	0.833	0.0000417	8146
Missense in Polyphen		189	307.26	0.61511		3452
Synonymous	-0.651	314	300	1.05	0.0000196	2357
Loss of Function	3.66	22	50.0	0.440	0.00000243	657

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000209	0.000209
Ashkenazi Jewish	0.00	0.00
East Asian	0.000282	0.000278
Finnish	0.000186	0.000186
European (Non-Finnish)	0.000243	0.000221
Middle Eastern	0.000282	0.000278
South Asian	0.0000993	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation. Overexpression causes down-regulation of a number of genes involved in the immune response. Some genes are also up-regulated (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.586
• rvis_EVS: -0.39
• rvis_percentile_EVS: 27.08

Haploinsufficiency Scores

• pHI: 0.0670
• hipred: Y
• hipred_score: 0.554
• ghis: 0.510

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.122

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfat
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; embryo phenotype; immune system phenotype; cellular phenotype

Gene ontology

• Biological process: hematopoietic progenitor cell differentiation;regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;spongiotrophoblast layer development
• Cellular component: nucleus;cytosol
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;metal ion binding