ZCRB1

zinc finger CCHC-type and RNA binding motif containing 1, the group of RNA binding motif containing|MicroRNA protein coding host genes|U11/U12 di-snRNP|Zinc fingers CCHC-type

Basic information

Region (hg38): 12:42312085-42326257

Links

ENSG00000139168 ∙ NCBI:85437 ∙ OMIM:610750 ∙ HGNC:29620 ∙ Uniprot:Q8TBF4 ∙ 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 ZCRB1 gene.

• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZCRB1 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						0
missense			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in ZCRB1

This is a list of pathogenic ClinVar variants found in the ZCRB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-42313743-C-G		not specified	Uncertain significance (Oct 06, 2021)
12-42313754-T-C		not specified	Uncertain significance (May 03, 2023)
12-42317880-A-T		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZCRB1	protein_coding	protein_coding	ENST00000266529	7	14041

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00355	0.958	125680	0	68	125748	0.000270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.962	82	110	0.743	0.00000553	1443
Missense in Polyphen		12	26.92	0.44577		404
Synonymous	-1.07	43	34.9	1.23	0.00000165	358
Loss of Function	1.81	6	13.0	0.460	7.15e-7	170

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000971	0.000961
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.000221	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000253	0.000246
Middle Eastern	0.000221	0.000217
South Asian	0.000423	0.000359
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Metabolism of RNA;mRNA Splicing - Minor Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.0989

Intolerance Scores

• loftool: 0.678
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.202
• hipred: N
• hipred_score: 0.352
• ghis: 0.552

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zcrb1

Gene ontology

• Biological process: mRNA splicing, via spliceosome;RNA splicing
• Cellular component: nucleoplasm;U12-type spliceosomal complex
• Molecular function: RNA binding;zinc ion binding