ZCCHC24

Summary

ZCCHC24 (zinc finger CCHC-type containing 24, HGNC:26911) is a protein-coding gene on chromosome 10q22.3, encoding Zinc finger CCHC domain-containing protein 24 (Q8N2G6).

Enables RNA binding activity.

Source: NCBI Gene 219654 — RefSeq curated summary.

At a glance

• GWAS associations: 18
• Clinical variants (ClinVar): 32 total
• MANE Select transcript: NM_153367

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26911
Approved symbol	ZCCHC24
Name	zinc finger CCHC-type containing 24
Location	10q22.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ90798, Z3CXXC8
Ensembl gene	ENSG00000165424
Ensembl biotype	protein_coding
Entrez	219654

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000372333, ENST00000372336, ENST00000944042

RefSeq mRNA: 1 — MANE Select: NM_153367 NM_153367

CCDS: CCDS7359

Canonical transcript exons

ENST00000372336 — 4 exons

Exon	Start	End
ENSE00001457566	79445195	79445624
ENSE00001771962	79382325	79386458
ENSE00003491424	79432558	79432758
ENSE00003605044	79394276	79394440

Expression profiles

Bgee: expression breadth ubiquitous, 283 present calls, max score 99.44.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.6236 / max 345.6380, expressed in 1509 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
110284	6.2564	1420
110283	5.2225	891
110282	0.1447	95

Top tissues by expression

294 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
inferior vagus X ganglion	UBERON:0005363	99.44	gold quality
middle frontal gyrus	UBERON:0002702	99.18	gold quality
subthalamic nucleus	UBERON:0001906	99.15	gold quality
lateral globus pallidus	UBERON:0002476	99.12	gold quality
inferior olivary complex	UBERON:0002127	99.09	gold quality
medulla oblongata	UBERON:0001896	99.02	gold quality
ventral tegmental area	UBERON:0002691	99.00	gold quality
olfactory bulb	UBERON:0002264	98.92	gold quality
substantia nigra pars reticulata	UBERON:0001966	98.90	gold quality
superior vestibular nucleus	UBERON:0007227	98.81	gold quality
dorsal plus ventral thalamus	UBERON:0001897	98.79	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	98.63	gold quality
globus pallidus	UBERON:0001875	98.41	gold quality
substantia nigra pars compacta	UBERON:0001965	98.40	gold quality
cranial nerve II	UBERON:0000941	98.39	gold quality
CA1 field of hippocampus	UBERON:0003881	98.27	gold quality
trigeminal ganglion	UBERON:0001675	98.23	gold quality
medial globus pallidus	UBERON:0002477	98.21	gold quality
pericardium	UBERON:0002407	98.03	gold quality
lateral nuclear group of thalamus	UBERON:0002736	97.82	gold quality
pons	UBERON:0000988	97.81	gold quality
spinal cord	UBERON:0002240	97.62	gold quality
dorsal root ganglion	UBERON:0000044	97.55	gold quality
midbrain	UBERON:0001891	97.53	gold quality
saphenous vein	UBERON:0007318	97.48	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	97.46	gold quality
substantia nigra	UBERON:0002038	97.37	gold quality
synovial joint	UBERON:0002217	97.26	gold quality
amygdala	UBERON:0001876	96.77	gold quality
urethra	UBERON:0000057	96.69	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-84465	yes	23.34
E-ANND-3	yes	16.44
E-GEOD-124858	no	102.69

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

260 targeting ZCCHC24, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-12121	99.99	66.64	255
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-LET-7F-2-3P	99.98	70.98	2588

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	zcchc24	ENSDARG00000078026
mus_musculus	Zcchc24	ENSMUSG00000055538
rattus_norvegicus	Zcchc24	ENSRNOG00000040205
caenorhabditis_elegans		WBGENE00012794

Paralogs (1): RBBP6 (ENSG00000122257)

Protein

Protein identifiers

Zinc finger CCHC domain-containing protein 24 — Q8N2G6 (reviewed: Q8N2G6)

All UniProt accessions (2): Q8N2G6, Q5W133

RefSeq proteins (1): NP_699198* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001878	Znf_CCHC	Domain
IPR025829	Zn_knuckle_CX2CX3GHX4C	Domain
IPR027377	ZAR1/RTP1-5-like_Znf-3CxxC	Domain
IPR033446	ZCCHC24_Znf-3CxxC	Domain
IPR036875	Znf_CCHC_sf	Homologous_superfamily
IPR057809	ZCCHC24_C	Domain

Pfam: PF13696, PF17180, PF23490

UniProt features (7 total): modified residue 2, sequence conflict 2, chain 1, zinc finger region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N2G6-F1	69.49	0.33

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 65, 93

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 282 (showing top): MYOGENIN_Q6, BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_DN, TTCCGTT_MIR191, PEREZ_TP63_TARGETS, MAZ_Q6, TATTATA_MIR374, CAGCTG_AP4_Q5, ATGTTAA_MIR302C, GTGCCTT_MIR506, CAIRO_HEPATOBLASTOMA_CLASSES_DN, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_DN, KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN, BROWNE_HCMV_INFECTION_14HR_DN, AAAGACA_MIR511

GO Biological Process (0):

GO Molecular Function (4): RNA binding (GO:0003723), zinc ion binding (GO:0008270), nucleic acid binding (GO:0003676), metal ion binding (GO:0046872)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nucleic acid binding	1
transition metal ion binding	1
binding	1
cation binding	1

Protein interactions and networks

STRING

648 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZCCHC24	RBM47	A0AV96	591
ZCCHC24	MFAP4	P55083	543
ZCCHC24	TMEM109	Q9BVC6	478
ZCCHC24	ESRP1	Q6NXG1	453
ZCCHC24	SH3RF3	Q8TEJ3	451
ZCCHC24	HYCC1	Q9BYI3	445
ZCCHC24	DYDC2	Q96IM9	440
ZCCHC24	ABCA8	O94911	437
ZCCHC24	ARRDC2	Q8TBH0	428
ZCCHC24	COL14A1	Q05707	421
ZCCHC24	ZNF423	Q2M1K9	420
ZCCHC24	COQ9	O75208	419
ZCCHC24	UHRF2	Q96PU4	412
ZCCHC24	USP49	Q70CQ1	407
ZCCHC24	GRHL1	Q9NZI5	404

IntAct

2 interactions, top by confidence:

A	B	Type	Score
LIN28A	GTPBP10	psi-mi:“MI:0914”(association)	0.350

BioGRID (9): ZCCHC24 (Affinity Capture-RNA), ZCCHC24 (Affinity Capture-RNA), ZCCHC24 (Affinity Capture-MS), ZCCHC24 (Proximity Label-MS), ZCCHC24 (Proximity Label-MS), ZCCHC24 (Affinity Capture-MS), ZCCHC24 (Cross-Linking-MS (XL-MS)), ZCCHC24 (Affinity Capture-RNA), ZCCHC24 (Two-hybrid)

ESM2 similar proteins: A0A1L8HBI7, A0A1L8HJK9, A0A1L8HTT5, A4QP16, A6NP61, B2RVL6, C0SPG1, C3VD30, K7SGN7, O54880, P56163, Q1XFL1, Q29RJ0, Q2KI52, Q32L09, Q3V0J4, Q4R2Y2, Q4R739, Q58D79, Q5RAK6, Q5TKR9, Q5VWQ0, Q6PDK8, Q768S4, Q7T3T8, Q7T3T9, Q80T69, Q86US8, Q86Y01, Q8AW93, Q8BMD7, Q8BRB7, Q8BZ21, Q8CAK3, Q8CDN1, Q8HXK7, Q8K3Y6, Q8N2G6, Q8N9V6, Q8TE76

Diamond homologs: B2RVL6, Q8HXK7, Q8N2G6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

32 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	22
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

833 predictions. Top by Δscore:

Variant	Effect	Δscore
10:79394270:GCTCA:G	donor_loss	1.0000
10:79394271:CTCA:C	donor_loss	1.0000
10:79394272:TCACC:T	donor_loss	1.0000
10:79394273:CACC:C	donor_loss	1.0000
10:79394274:A:C	donor_loss	1.0000
10:79394275:C:T	donor_loss	1.0000
10:79394275:CCTG:C	donor_gain	1.0000
10:79432552:CCTTA:C	donor_loss	1.0000
10:79432553:CTTA:C	donor_loss	1.0000
10:79432554:TTACC:T	donor_loss	1.0000
10:79432555:TAC:T	donor_loss	1.0000
10:79432556:A:AC	donor_gain	1.0000
10:79432556:A:AT	donor_loss	1.0000
10:79432556:AC:A	donor_gain	1.0000
10:79432557:C:CC	donor_gain	1.0000
10:79432557:CC:C	donor_gain	1.0000
10:79432557:CCTGG:C	donor_gain	1.0000
10:79432754:AGCGC:A	acceptor_gain	1.0000
10:79432755:GCGC:G	acceptor_gain	1.0000
10:79432756:CGC:C	acceptor_gain	1.0000
10:79432756:CGCC:C	acceptor_gain	1.0000
10:79432757:GC:G	acceptor_gain	1.0000
10:79432757:GCCT:G	acceptor_loss	1.0000
10:79432758:CC:C	acceptor_gain	1.0000
10:79432759:C:CC	acceptor_gain	1.0000
10:79432760:T:G	acceptor_loss	1.0000
10:79445190:CCCA:C	donor_loss	1.0000
10:79445191:CCAC:C	donor_loss	1.0000
10:79445192:CACC:C	donor_loss	1.0000
10:79445193:A:AG	donor_loss	1.0000

AlphaMissense

1575 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:79386359:G:A	R238C	1.000
10:79386359:G:T	R238S	1.000
10:79386360:G:C	C237W	1.000
10:79386361:C:A	C237F	1.000
10:79386361:C:G	C237S	1.000
10:79386361:C:T	C237Y	1.000
10:79386362:A:G	C237R	1.000
10:79386362:A:T	C237S	1.000
10:79386370:C:A	G234V	1.000
10:79386370:C:T	G234D	1.000
10:79386371:C:A	G234C	1.000
10:79386371:C:G	G234R	1.000
10:79386373:A:G	L233P	1.000
10:79386381:G:C	C230W	1.000
10:79386382:C:A	C230F	1.000
10:79386382:C:G	C230S	1.000
10:79386382:C:T	C230Y	1.000
10:79386383:A:G	C230R	1.000
10:79386383:A:T	C230S	1.000
10:79386384:C:A	K229N	1.000
10:79386384:C:G	K229N	1.000
10:79386390:G:C	C227W	1.000
10:79386391:C:A	C227F	1.000
10:79386391:C:G	C227S	1.000
10:79386391:C:T	C227Y	1.000
10:79386392:A:C	C227G	1.000
10:79386392:A:G	C227R	1.000
10:79386392:A:T	C227S	1.000
10:79386394:A:G	L226P	1.000
10:79386394:A:T	L226H	1.000

dbSNP variants (sampled 300 via entrez): RS1000117515 (10:79405388 A>T), RS1000125339 (10:79431236 C>G), RS1000218655 (10:79442103 G>A,C), RS1000245471 (10:79422356 T>G), RS1000251346 (10:79435984 A>G), RS1000258998 (10:79396521 C>T), RS1000314051 (10:79410465 C>T), RS1000499267 (10:79431008 A>G), RS1000512360 (10:79395294 G>A), RS1000530370 (10:79440449 T>A), RS1000533045 (10:79390677 T>C), RS1000588633 (10:79416130 A>T), RS1000591779 (10:79441788 A>T), RS1000651407 (10:79394869 A>T), RS1000684210 (10:79446745 G>A,C,T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

18 associations (top):

Study	Trait	p-value
GCST002647_38	Height	5.000000e-24
GCST002960_4	Frontotemporal dementia	5.000000e-06
GCST003814_24	Selective IgA deficiency	7.000000e-06
GCST004351_27	Bone ultrasound measurement (broadband ultrasound attenuation)	4.000000e-07
GCST004603_53	Platelet count	3.000000e-10
GCST004607_118	Plateletcrit	1.000000e-10
GCST006979_594	Heel bone mineral density	3.000000e-15
GCST008163_174	Height	1.000000e-07
GCST008839_474	Height	4.000000e-18
GCST010241_253	Apolipoprotein A1 levels	5.000000e-08
GCST012420_7	tricyclic pyrone compound response (IC50)	5.000000e-06
GCST90002385_486	High light scatter reticulocyte count	6.000000e-09
GCST90002386_407	High light scatter reticulocyte percentage of red cells	3.000000e-09
GCST90002400_711	Plateletcrit	3.000000e-16
GCST90002402_123	Platelet count	1.000000e-16
GCST90013466_10	Height	2.000000e-31
GCST90013466_31	Height	7.000000e-10
GCST90013468_17	Height	2.000000e-08

EFO canonical traits (7, from GWAS)

EFO ID	Trait name
EFO:0004514	bone quantitative ultrasound measurement
EFO:0004309	platelet count
EFO:0007985	platelet crit
EFO:0009270	heel bone mineral density
EFO:0004614	apolipoprotein A 1 measurement
EFO:0600033	response to mitochondrial complex I inhibitor
EFO:0007986	reticulocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

43 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
trichostatin A	affects cotreatment, increases expression, affects expression	3
(+)-JQ1 compound	increases expression	3
Benzo(a)pyrene	affects methylation, decreases expression, decreases methylation, increases methylation	3
Valproic Acid	decreases methylation, increases expression	3
Silicon Dioxide	decreases expression, increases expression	2
Smoke	decreases expression, increases expression	2
Tobacco Smoke Pollution	decreases expression	2
Tretinoin	decreases expression, increases expression	2
Raloxifene Hydrochloride	affects expression, affects cotreatment, decreases expression	2
afuresertib	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	increases methylation	1
methylselenic acid	increases expression	1
arsenite	affects binding, decreases reaction	1
sodium arsenite	increases expression	1
aflatoxin B2	increases methylation	1
S-(1,2-dichlorovinyl)cysteine	decreases expression, affects response to substance, increases expression, affects cotreatment	1
tamibarotene	increases expression	1
cylindrospermopsin	decreases expression	1
monomethylarsonous acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine	decreases expression, increases response to substance	1
Resveratrol	decreases expression, affects cotreatment	1
Temozolomide	decreases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Atrazine	increases expression	1
Formaldehyde	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.