ZFC3H1

protein-coding

zinc finger C3H1-type containing, the group of Zinc fingers

Gene summary

Predicted to enable zinc ion binding activity. Predicted to be involved in RNA catabolic process. Located in nucleus. Part of MTREC complex. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

PSRC2
CCDC131

MANE transcript

NM_144982.5

Inheritance

—

ClinVar variants

P:2U:234B:13

Top phenotype

Short stature

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr12:71,609,599-71,667,725

External References & Databases

Ensembl (ENSG00000133858)

Transcript & Mutation Effects

hg38 • Region Span ~58.1 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 ZFC3H1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 225

not providedTotal: 11

Short statureTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_144982.5. 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	4 clinvar	7 clinvar	12
missense		2 clinvar	230 clinvar	2 clinvar		234
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	2	234	6	7	249

Highest pathogenic variant AF is 0.000095440664

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_144982.5	RefSeq	NP_659419.3	35	MANE Select
ENST00000378743.9	Ensembl	ENSP00000368017.4	35	MANE Select
ENST00000548100.1	Ensembl	ENSP00000450044.1	2	Standard
ENST00000548100.2	Ensembl	ENSP00000450044.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

RNA processing

Molecular Function

RNA binding
protein binding
metal ion binding

Cellular Component

exosome (RNase complex)
extracellular space
nucleus
nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000378743
Coding exons: 35
Length: 58254
Individuals with no LoFs: 124780
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 124794
p: 0.0000561

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.14	785	973	0.807	0.0000482	13018
Missense (PolyPhen)		190	333.16	0.5703		4547
Synonymous	-1.27	379	349	1.09	0.0000170	3693
Loss of Function	8.73	10	108	0.0928	0.00000578	1365

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000030	0.000029	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0	0.0	absent
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.000073	0.000071	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Subunit of the trimeric poly(A) tail exosome targeting (PAXT) complex, a complex that directs a subset of long and polyadenylated poly(A) RNAs for exosomal degradation. The RNA exosome is fundamental for the degradation of RNA in eukaryotic nuclei. Substrate targeting is facilitated by its cofactor MTREX, which links to RNA-binding protein adapters. {ECO:0000269|PubMed:27871484}.;

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.220
RVIS EVS: -1.83
RVIS percentile EVS: 2.12

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.954

Gene Damage Prediction

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