ZC3H12C

protein-coding

zinc finger CCCH-type containing 12C, the group of Zinc fingers CCCH-type

Gene summary

Predicted to enable RNA endonuclease activity and mRNA binding activity. Predicted to be involved in 3'-UTR-mediated mRNA destabilization. Predicted to be active in cytoplasmic ribonucleoprotein granule and nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_033390.2

Inheritance

—

ClinVar variants

U:108B:6

Top phenotype

X-linked Alport syndrome

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chr11:110,093,392-110,171,841

External References & Databases

Ensembl (ENSG00000149289)

Transcript & Mutation Effects

hg38 • Region Span ~78.4 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 ZC3H12C variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 107

not providedTotal: 1

X-linked Alport syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_033390.2. 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						0
missense			107 clinvar	6 clinvar		113
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	108	6	0	114

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_033390.2	RefSeq	NP_203748.1	6	MANE Select
ENST00000278590.8	Ensembl	ENSP00000278590.3	6	MANE Select
NM_001411037.1	RefSeq	NP_001397966.1	6	Standard
ENST00000453089.2	Ensembl	ENSP00000413094.2	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process
nucleic acid phosphodiester bond hydrolysis

Molecular Function

molecular_function
endonuclease activity
metal ion binding

Cellular Component

cellular_component

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000278590
Coding exons: 6
Length: 78480
Individuals with no LoFs: 124886
Homozygous LoFs: 2
Heterozygous LoFs: 50
Defined: 124938
p: 0.000208

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.80	377	489	0.771	0.0000268	5810
Missense (PolyPhen)		108	206.43	0.52317		2440
Synonymous	1.69	158	187	0.843	0.0000111	1694
Loss of Function	4.97	4	36.4	0.110	0.00000234	418

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00026	0.00026	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00018	0.00017	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00012	0.00012	rare
South Asian	0.00075	0.00069	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May function as RNase and regulate the levels of target RNA species. {ECO:0000305}.;

Recessive Scores

pRec: 0.107

Intolerance Scores

LoFtool: 0.402
RVIS EVS: -0.73
RVIS percentile EVS: 14.14

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): K
Indispensability pred.: N
Indispensability score: 0.318

Gene Damage Prediction

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