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
• intellectual developmental disorder, autosomal dominant 64 (Strong), 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.

• Inborn_genetic_diseases (315 variants)
• not_provided (293 variants)
• Intellectual_developmental_disorder,_autosomal_dominant_64 (115 variants)
• ZNF292-related_disorder (67 variants)
• Neurodevelopmental_disorder (35 variants)
• not_specified (27 variants)
• Intellectual_disability (9 variants)
• See_cases (3 variants)
• Complex_neurodevelopmental_disorder (2 variants)
• Motor_delay (1 variants)
• Intellectual_disability,_mild (1 variants)
• Neurodevelopmental_delay (1 variants)
• Microcephaly (1 variants)
• ZNF292-related_neurodevelopmental_condition (1 variants)
• Autism (1 variants)
• Autosomal_dominant_non-syndromic_intellectual_disability (1 variants)
• Short_stature (1 variants)
• Arterial_calcification,_generalized,_of_infancy,_1 (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. These statistics are base on transcript: NM_000015021.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			3	55	8	66
missense		6	386	143	10	545
nonsense	13	24	5			42
start loss			1			1
frameshift	23	39	9	1		72
splice donor/acceptor (+/-2bp)			1			1
Total	36	69	405	199	18

Highest pathogenic variant AF is 0.00002194338

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