ZCCHC24

protein-coding

zinc finger CCHC-type containing 24, the group of Zinc fingers 3CxxC-type|Zinc fingers CCHC-type

Gene summary

Enables RNA binding activity. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C10orf56

MANE transcript

NM_153367.4

Inheritance

—

ClinVar variants

U:26

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr10:79,382,325-79,445,624

External References & Databases

Ensembl (ENSG00000165424)

Transcript & Mutation Effects

hg38 • Region Span ~63.3 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 ZCCHC24 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 23

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153367.4. 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			1 clinvar			1
missense			24 clinvar			24
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	26	0	0	26

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_153367.4	RefSeq	NP_699198.2	4	MANE Select
ENST00000372336.4	Ensembl	ENSP00000361411.3	4	MANE Select
ENST00000372333.3	Ensembl	ENSP00000361408.3	4	Standard
ENST00000944042.1	Ensembl	ENSP00000614101.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

RNA binding
zinc ion binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372336
Coding exons: 4
Length: 63303
Individuals with no LoFs: 120072
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 120073
p: 0.00000416

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.91	69	130	0.530	0.00000802	1558
Missense (PolyPhen)		38	74.024	0.51335		790
Synonymous	0.201	57	59.0	0.967	0.00000395	457
Loss of Function	2.78	0	9.01	0.00	3.83e-7	126

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000030	0.000030	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.116

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.307

Gene Damage Prediction

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