ZNF699

protein-coding

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

Gene summary

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_198535.3

Inheritance

ClinVar variants

P:15U:76B:13

Top phenotype

Developmental delay with gastrointestinal, cardiovascular, genitourinary, and skeletal abnormalities (DEGCAGS syndrome)

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr19:9,291,140-9,309,838

External References & Databases

Ensembl (ENSG00000196110)

Transcript & Mutation Effects

hg38 • Region Span ~18.7 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

DEGCAGS syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0859181

Submitter: PanelApp Australia

DEGCAGS syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0859181

Submitter: Ambry Genetics

DEGCAGS syndromeMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0859181

Submitter: Ambry Genetics

DEGCAGS syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0859181

Submitter: Labcorp Genetics (formerly Invitae)

DEGCAGS syndromeMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0859181

Submitter: G2P

Clinical Genomic Database (CGD)

Developmental delay with gastrointestinal, cardiovascular, genitourinary, and skeletal abnormalities (DEGCAGS syndrome)AR

Manifestation: Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Cardiovascular; Craniofacial; Gastrointestinal; Genitourinary; Hematologic; Musculoskeletal; Neurologic

Intervention: Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Hematologic;

Rationale: 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

Refs: 33875846

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZNF699 variants in ClinVar

6 Conditions Cataloged

Inborn genetic diseasesTotal: 69

DEGCAGS syndromeTotal: 26

not providedTotal: 16

ZNF699-related disorderTotal: 2

Diamond-Blackfan anemiaTotal: 1

not specifiedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198535.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				9 clinvar		9
missense			73 clinvar	3 clinvar		76
nonsense	1 clinvar	3 clinvar	1 clinvar			5
start loss			1 clinvar			1
frameshift	8 clinvar	2 clinvar	1 clinvar	1 clinvar		12
splice donor/acceptor (+/-2bp)		1 clinvar				1
Total	9	6	76	13	0	104

Highest pathogenic variant AF is 0.000033500415

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_198535.3	RefSeq	NP_940937.1	5	MANE Select
ENST00000591998.6	Ensembl	ENSP00000467723.1	5	MANE Select
ENST00000308650.4	Ensembl	ENSP00000311596.3	5	Standard
ENST00000952100.1	Ensembl	ENSP00000622159.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gene expression (Transcription)
Generic Transcription Pathway
RNA Polymerase II Transcription

Biological Process

regulation of transcription by RNA polymerase II

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
protein binding
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000591998
Coding exons: 5
Length: 15564
Individuals with no LoFs: 125693
Homozygous LoFs: 0
Heterozygous LoFs: 30
Defined: 125723
p: 0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.851	293	337	0.870	0.0000159	4283
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000064	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00018	0.00017	rare
South Asian	0.00013	0.00013	rare
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation.;

Recessive Scores

pRec: 0.116

Intolerance Scores

LoFtool: 0.644
RVIS EVS: -0.31
RVIS percentile EVS: 32.06

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.315

Gene Damage Prediction

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