ZNF292

zinc finger protein 292, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 6:87151803-87265943

Links

ENSG00000188994 ∙ NCBI:23036 ∙ OMIM:616213 ∙ HGNC:18410 ∙ Uniprot:O60281 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Definitive), mode of inheritance: AD
• intellectual developmental disorder, autosomal dominant 64 (Strong), mode of inheritance: AD
• complex neurodevelopmental disorder (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, autosomal dominant 64	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	31723249

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF292 gene.

• Intellectual developmental disorder, autosomal dominant 64 (9 variants)
• not provided (8 variants)
• Neurodevelopmental disorder (8 variants)
• Inborn genetic diseases (7 variants)
• Intellectual disability (1 variants)
• Neurodevelopmental delay (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF292 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	44	10	56
missense		4	212	83	13	312
nonsense	10	13	4			27
start loss			1			1
frameshift	13	23	8	1		45
inframe indel			7	2		9
splice donor/acceptor (+/-2bp)			1			1
splice region			3	1	1	5
non coding						0
Total	23	40	235	130	23

Highest pathogenic variant AF is 0.00000658

Variants in ZNF292

This is a list of pathogenic ClinVar variants found in the ZNF292 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-87155593-T-G		Intellectual developmental disorder, autosomal dominant 64	Uncertain significance (Mar 14, 2023)
6-87155610-G-A		ZNF292-related disorder	Uncertain significance (Nov 22, 2023)
6-87155630-C-T		ZNF292-related disorder	Likely benign (Apr 04, 2022)
6-87155631-G-A		Inborn genetic diseases	Uncertain significance (Sep 16, 2021)
6-87155638-G-C		Inborn genetic diseases	Uncertain significance (Dec 29, 2020)
6-87155639-C-A			Likely benign (May 01, 2024)
6-87155649-G-A		Inborn genetic diseases	Likely benign (Jul 02, 2021)
6-87155652-G-A		Intellectual developmental disorder, autosomal dominant 64	Uncertain significance (Jun 04, 2024)
6-87155652-G-C		Intellectual developmental disorder, autosomal dominant 64	Likely pathogenic (Aug 21, 2023)
6-87155659-A-C		Inborn genetic diseases	Likely benign (Dec 01, 2023)
6-87155670-G-C			Uncertain significance (Feb 21, 2023)
6-87155673-C-T			Uncertain significance (Oct 17, 2019)
6-87155709-C-T			Uncertain significance (Aug 08, 2019)
6-87155763-A-T			Uncertain significance (Apr 12, 2024)
6-87169700-G-T			Likely benign (Jul 01, 2024)
6-87215909-C-G		Inborn genetic diseases	Uncertain significance (Jul 27, 2022)
6-87215918-G-A		ZNF292-related disorder	Uncertain significance (Jun 13, 2024)
6-87215923-G-C			Uncertain significance (Aug 01, 2022)
6-87215999-C-T		Intellectual disability • Neurodevelopmental disorder • Intellectual developmental disorder, autosomal dominant 64	Pathogenic/Likely pathogenic (May 17, 2023)
6-87216003-C-G		Inborn genetic diseases	Uncertain significance (Apr 12, 2022)
6-87216028-T-G		Inborn genetic diseases	Uncertain significance (Apr 18, 2023)
6-87216058-G-A		Intellectual developmental disorder, autosomal dominant 64	Uncertain significance (Jan 27, 2020)
6-87216299-A-G		Inborn genetic diseases	Likely benign (Apr 16, 2024)
6-87216327-C-T		See cases	Uncertain significance (Sep 03, 2021)
6-87218599-G-A		Intellectual developmental disorder, autosomal dominant 64	Uncertain significance (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF292	protein_coding	protein_coding	ENST00000369577	8	111364

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.09e-10	124585	0	27	124612	0.000108

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.41	1203	1.35e+3	0.892	0.0000667	17948
Missense in Polyphen		202	433.73	0.46572		5788
Synonymous	-2.14	553	493	1.12	0.0000247	5096
Loss of Function	8.30	7	93.8	0.0747	0.00000516	1306

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000194	0.000194
Ashkenazi Jewish	0.0000995	0.0000994
East Asian	0.00	0.00
Finnish	0.000372	0.000371
European (Non-Finnish)	0.000125	0.0000974
Middle Eastern	0.00	0.00
South Asian	0.0000994	0.0000980
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.151

Intolerance Scores

• loftool: 0.282
• rvis_EVS: -1.15
• rvis_percentile_EVS: 6.29

Haploinsufficiency Scores

• pHI: 0.922
• hipred: N
• hipred_score: 0.390
• ghis: 0.610

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.776

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp292

Gene ontology

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