ZFC3H1

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

Basic information

Region (hg38): 12:71609599-71667725

Previous symbols: [ "PSRC2", "CCDC131" ]

Links

ENSG00000133858 ∙ NCBI:196441 ∙ ∙ HGNC:28328 ∙ Uniprot:O60293 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZFC3H1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZFC3H1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	6	8
missense			78	1		79
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	78	3	6

Variants in ZFC3H1

This is a list of pathogenic ClinVar variants found in the ZFC3H1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-71610453-T-A		not specified	Uncertain significance (Jun 09, 2022)
12-71610513-A-G		Short stature	Likely pathogenic (Nov 18, 2001)
12-71611075-G-C		not specified	Uncertain significance (Jun 03, 2022)
12-71613389-T-C		not specified	Uncertain significance (Mar 29, 2024)
12-71615271-T-C			Benign (Dec 31, 2019)
12-71615275-C-T		not specified	Uncertain significance (Jul 26, 2022)
12-71619379-G-A		not specified	Uncertain significance (Feb 28, 2024)
12-71619930-A-G		not specified	Uncertain significance (Apr 07, 2022)
12-71619933-A-T		not specified	Uncertain significance (Mar 03, 2022)
12-71619947-C-T		not specified	Uncertain significance (Feb 05, 2024)
12-71619960-A-G		not specified	Uncertain significance (Jan 24, 2024)
12-71619975-G-T		not specified	Uncertain significance (Jun 24, 2022)
12-71619978-T-A		not specified	Uncertain significance (Jun 22, 2021)
12-71620011-G-A		not specified	Uncertain significance (May 26, 2024)
12-71620015-T-C		not specified	Uncertain significance (Apr 05, 2023)
12-71620292-C-T		not specified	Uncertain significance (Nov 13, 2023)
12-71620297-G-C		not specified	Uncertain significance (Jan 23, 2024)
12-71620315-T-C		not specified	Uncertain significance (Dec 01, 2022)
12-71623506-A-G		not specified	Uncertain significance (Dec 14, 2023)
12-71623522-C-A		not specified	Uncertain significance (Sep 07, 2022)
12-71623584-G-A		not specified	Uncertain significance (Aug 26, 2022)
12-71624143-T-C		not specified	Uncertain significance (Dec 28, 2023)
12-71626323-G-A			Benign (Aug 20, 2018)
12-71626402-C-T		not specified	Uncertain significance (Aug 26, 2022)
12-71627753-C-G		not specified	Uncertain significance (May 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZFC3H1	protein_coding	protein_coding	ENST00000378743	35	58254

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	8.17e-11	124780	0	14	124794	0.0000561

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.14	785	973	0.807	0.0000482	13018
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000296	0.0000296
Ashkenazi Jewish	0.000102	0.0000993
East Asian	0.00	0.00
Finnish	0.000141	0.000139
European (Non-Finnish)	0.0000728	0.0000706
Middle Eastern	0.00	0.00
South Asian	0.0000334	0.0000327
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.545
• hipred: Y
• hipred_score: 0.625
• ghis: 0.604

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.954

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfc3h1

Gene ontology

• Biological process: RNA processing
• Cellular component: exosome (RNase complex);extracellular space;nucleus;nucleolus
• Molecular function: RNA binding;protein binding;metal ion binding