ZNF236

protein-coding

zinc finger protein 236, 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. Involved in cellular response to glucose stimulus. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001306089.2

Inheritance

—

ClinVar variants

U:229B:32

Top phenotype

Neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr18:76,822,557-76,972,901

External References & Databases

Ensembl (ENSG00000130856)

Transcript & Mutation Effects

hg38 • Region Span ~150.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZNF236 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 216

not providedTotal: 25

Neurodevelopmental disorderTotal: 2

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001306089.2. 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			4 clinvar	4 clinvar	9 clinvar	17
missense			215 clinvar	17 clinvar	2 clinvar	234
nonsense			3 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	229	21	11	261

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001306089.2	RefSeq	NP_001293018.1	31	MANE Select
ENST00000320610.14	Ensembl	ENSP00000322361.9	31	MANE Select
NM_007345.4	RefSeq	NP_031371.3	31	Standard
ENST00000253159.12	Ensembl	ENSP00000253159.8	31	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription, DNA-templated
regulation of transcription by RNA polymerase II
cellular response to glucose stimulus

Molecular Function

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000253159
Coding exons: 31
Length: 148121
Individuals with no LoFs: 124903
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 124917
p: 0.0000560

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.84	743	1.10e+3	0.675	0.0000678	12163
Missense (PolyPhen)		187	390.02	0.47947		4250
Synonymous	-0.165	462	458	1.01	0.0000322	3525
Loss of Function	7.75	8	85.2	0.0939	0.00000435	1003

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00026	0.00026	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.000071	0.000071	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.102

Intolerance Scores

LoFtool: 0.165
RVIS EVS: -1.53
RVIS percentile EVS: 3.35

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.294

Gene Damage Prediction

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