ZNF683

zinc finger protein 683, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 1:26361634-26374522

Links

ENSG00000176083 ∙ NCBI:257101 ∙ OMIM:616775 ∙ HGNC:28495 ∙ Uniprot:Q8IZ20 ∙ 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 ZNF683 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF683 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			44	3		47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	5	0

Variants in ZNF683

This is a list of pathogenic ClinVar variants found in the ZNF683 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-26361686-T-C		not specified	Uncertain significance (Apr 09, 2024)
1-26361719-T-C		not specified	Uncertain significance (Oct 13, 2023)
1-26361733-G-A		not specified	Likely benign (Mar 25, 2024)
1-26361736-G-A		not specified	Uncertain significance (Jan 24, 2024)
1-26361739-A-G		not specified	Uncertain significance (Jul 19, 2022)
1-26361740-C-A		not specified	Uncertain significance (Feb 17, 2023)
1-26361796-T-C		not specified	Uncertain significance (Jul 14, 2024)
1-26361797-C-A		not specified	Uncertain significance (Jan 04, 2024)
1-26361853-G-A		not specified	Uncertain significance (May 13, 2024)
1-26361866-C-T		not specified	Likely benign (Jan 31, 2024)
1-26361907-T-G		not specified	Uncertain significance (Sep 02, 2024)
1-26361915-C-G		not specified	Uncertain significance (Mar 18, 2024)
1-26361931-C-T		not specified	Uncertain significance (Jan 04, 2024)
1-26361953-G-T		not specified	Uncertain significance (Dec 21, 2022)
1-26361955-C-T		not specified	Uncertain significance (Oct 12, 2024)
1-26361962-C-T		not specified	Uncertain significance (Jun 02, 2023)
1-26363049-C-T		not specified	Uncertain significance (Jun 03, 2024)
1-26363128-C-A		not specified	Uncertain significance (Oct 03, 2022)
1-26363135-C-T		not specified	Uncertain significance (Aug 21, 2023)
1-26363144-C-T		not specified	Uncertain significance (Apr 29, 2024)
1-26363145-G-A		not specified	Uncertain significance (Mar 07, 2025)
1-26364556-G-T		not specified	Uncertain significance (May 18, 2023)
1-26364574-G-C		not specified	Uncertain significance (Sep 29, 2023)
1-26364575-C-T		not specified	Uncertain significance (Sep 30, 2021)
1-26364623-G-C		not specified	Uncertain significance (May 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF683	protein_coding	protein_coding	ENST00000374204	5	12889

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.12e-7	0.348	125351	0	15	125366	0.0000598

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.101	284	279	1.02	0.0000154	3233
Missense in Polyphen		58	67.625	0.85767		895
Synonymous	0.698	109	119	0.918	0.00000638	1062
Loss of Function	0.609	12	14.5	0.827	7.78e-7	163

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000556	0.000549
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000549	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000277	0.0000265
Middle Eastern	0.0000549	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor that mediates a transcriptional program in various innate and adaptive immune tissue-resident lymphocyte T-cell types such as tissue-resident memory T (Trm), natural killer (trNK) and natural killer T (NKT) cells and negatively regulates gene expression of proteins that promote the egress of tissue-resident T-cell populations from non-lymphoid organs. Plays a role in the development, retention and long-term establishment of adaptive and innate tissue-resident lymphocyte T cell types in non-lymphoid organs, such as the skin and gut, but also in other nonbarrier tissues like liver and kidney, and therefore may provide immediate immunological protection against reactivating infections or viral reinfection. Plays also a role in the differentiation of both thymic and peripheral NKT cells. Negatively regulates the accumulation of interferon-gamma (IFN- gamma) in NKT cells at steady state or after antigenic stimulation. Positively regulates granzyme B production in NKT cells after innate stimulation. Associates with the transcriptional repressor PRDM1/BLIMP1 to chromatin at gene promoter regions. {ECO:0000250|UniProtKB:I7HJS4}.; FUNCTION: Isoform 2: Transcriptional repressor that binds to DNA within promoter regions of the transcriptional repressor PRDM1/BLIMP1 target sites. Regulates interferon-gamma (IFN-gamma) production in cytomegalovirus (CMV)-infected effector CD8(+) T cells. {ECO:0000269|PubMed:26179882}.

Intolerance Scores

• loftool: 0.992
• rvis_EVS: 1.09
• rvis_percentile_EVS: 91.9

Haploinsufficiency Scores

• pHI: 0.113
• hipred: N
• hipred_score: 0.123
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.555

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp683
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: adaptive immune response;regulation of transcription by RNA polymerase II;regulation of gene expression;regulation of natural killer cell differentiation;regulation of natural killer cell differentiation involved in immune response;regulation of extrathymic T cell differentiation;innate immune response;regulation of NK T cell differentiation
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding;promoter-specific chromatin binding