ZNF699

zinc finger protein 699, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:9291139-9309838

Links

ENSG00000196110 ∙ NCBI:374879 ∙ OMIM:609571 ∙ HGNC:24750 ∙ Uniprot:Q32M78 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• DEGCAGS syndrome (Moderate), mode of inheritance: AR
• DEGCAGS syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
DEGCAGS syndrome	AR	Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Hematologic;	Among other manifestations, the condition may include immunodeficiency and increased risk of infections, and awareness may allow preventative measures and early and aggressive treatment of infections	Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Cardiovascular; Craniofacial; Gastrointestinal; Genitourinary; Hematologic; Musculoskeletal; Neurologic	33875846

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF699 gene.

• DEGCAGS syndrome (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF699 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			28	3		31
nonsense			1			1
start loss			1			1
frameshift	2	1		1		4
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	2	1	31	4	0

Variants in ZNF699

This is a list of pathogenic ClinVar variants found in the ZNF699 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-9295506-T-G		Inborn genetic diseases	Uncertain significance (Oct 05, 2023)
19-9295513-G-A		not specified	Uncertain significance (Mar 21, 2023)
19-9295575-G-T		Inborn genetic diseases	Uncertain significance (Jun 03, 2024)
19-9295596-C-T		Inborn genetic diseases	Uncertain significance (May 01, 2024)
19-9295699-G-A		Inborn genetic diseases	Uncertain significance (Feb 10, 2022)
19-9295725-T-G		Inborn genetic diseases	Uncertain significance (Nov 21, 2022)
19-9295749-G-A		Inborn genetic diseases	Uncertain significance (Aug 04, 2022)
19-9295762-T-G		Inborn genetic diseases	Uncertain significance (Jan 29, 2024)
19-9295768-G-C		Inborn genetic diseases	Uncertain significance (May 23, 2024)
19-9295771-C-T		Inborn genetic diseases	Uncertain significance (Mar 15, 2024)
19-9295777-GATAA-G		DEGCAGS syndrome	Likely benign (Apr 04, 2024)
19-9295870-A-G			Uncertain significance (Mar 30, 2023)
19-9295899-G-A		Inborn genetic diseases	Uncertain significance (Mar 21, 2023)
19-9295911-CTG-C		DEGCAGS syndrome	Pathogenic (Jul 17, 2023)
19-9296010-T-C		Inborn genetic diseases	Uncertain significance (May 24, 2024)
19-9296025-G-A		Inborn genetic diseases	Uncertain significance (May 16, 2024)
19-9296076-C-T		Inborn genetic diseases	Uncertain significance (Mar 30, 2023)
19-9296079-C-CT		DEGCAGS syndrome	Pathogenic (Aug 18, 2021)
19-9296092-CAT-C		DEGCAGS syndrome	Pathogenic (Aug 26, 2022)
19-9296151-G-A		Inborn genetic diseases	Uncertain significance (Apr 25, 2023)
19-9296176-T-C		Inborn genetic diseases	Uncertain significance (Aug 13, 2021)
19-9296224-T-C		Inborn genetic diseases	Uncertain significance (Jul 08, 2022)
19-9296227-A-G		Inborn genetic diseases	Uncertain significance (Aug 02, 2021)
19-9296262-T-C		Inborn genetic diseases	Uncertain significance (Jan 04, 2024)
19-9296302-ACT-A		ZNF699-related disorder	Likely pathogenic (Jun 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF699	protein_coding	protein_coding	ENST00000591998	5	15564

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000577	0.972	125693	0	30	125723	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.851	293	337	0.870	0.0000159	4283
Missense in Polyphen		107	129.36	0.82717		1638
Synonymous	1.61	99	122	0.814	0.00000623	1114
Loss of Function	2.02	12	22.3	0.538	9.91e-7	349

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000122	0.000119
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000177	0.000167
Middle Eastern	0.00	0.00
South Asian	0.000132	0.000131
Other	0.000500	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.644
• rvis_EVS: -0.31
• rvis_percentile_EVS: 32.06

Haploinsufficiency Scores

• pHI: 0.0795
• hipred: N
• hipred_score: 0.112
• ghis: 0.563

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.315

Gene Damage Prediction

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

Gene ontology

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