ZNHIT1

protein-coding

zinc finger HIT-type containing 1, the group of Zinc fingers HIT-type|SRCAP complex

Gene summary

Enables histone binding activity. Involved in muscle cell differentiation and positive regulation of DNA damage response, signal transduction by p53 class mediator. Located in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

ZNFN4A1

MANE transcript

NM_006349.3

Inheritance

—

ClinVar variants

U:26

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.92

Max pathogenic AF

—

Genomic locus

chr7:101,218,165-101,224,190

External References & Databases

Ensembl (ENSG00000106400)

Transcript & Mutation Effects

hg38 • Region Span ~6.0 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 ZNHIT1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 22

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006349.3. 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						0
missense			23 clinvar			23
nonsense						0
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	26	0	0	26

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006349.3	RefSeq	NP_006340.1	5	MANE Select
ENST00000305105.3	Ensembl	ENSP00000304593.2	5	MANE Select
ENST00000890490.1	Ensembl	ENSP00000560549.1	4	Standard
ENST00000956465.1	Ensembl	ENSP00000626524.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of histone deacetylation
histone exchange

Molecular Function

protein binding
nucleosome binding
histone deacetylase binding
metal ion binding

Cellular Component

Swr1 complex
nucleus
nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000305105
Coding exons: 5
Length: 6523
Individuals with no LoFs: 125691
Homozygous LoFs: 0
Heterozygous LoFs: 57
Defined: 125748
p: 0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.12	76	109	0.697	0.00000784	984
Missense (PolyPhen)		15	27.803	0.53951		299
Synonymous	-0.202	45	43.3	1.04	0.00000282	310
Loss of Function	0.237	9	9.80	0.918	5.89e-7	96

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.00099	0.00098	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00012	rare
South Asian	0.000098	0.000098	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Seems to play a role in p53-mediated apoptosis induction. Binds to NR1D2 and relieves it of its inhibitory effect on the transcription of APOC3 without affecting its DNA-binding activity. {ECO:0000269|PubMed:17380123, ECO:0000269|PubMed:17892483}.;

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.545
RVIS EVS: -0.32
RVIS percentile EVS: 31.46

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.264

Gene Damage Prediction

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