ZRSR2

zinc finger CCCH-type, RNA binding motif and serine/arginine rich 2, the group of U11/U12 di-snRNP|Zinc fingers CCCH-type|RNA binding motif containing

Basic information

Region (hg38): X:15790155-15830694

Previous symbols: [ "U2AF1L2" ]

Links

ENSG00000169249 ∙ NCBI:8233 ∙ OMIM:300028 ∙ HGNC:23019 ∙ Uniprot:Q15696 ∙ 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 ZRSR2 gene.

• Inborn genetic diseases (11 variants)
• not provided (8 variants)
• not specified (6 variants)
• Median cleft lip and palate;Heart, malformation of;Holoprosencephaly sequence;Severe hydrocephalus (1 variants)
• Pettigrew syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZRSR2 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	1	3
missense			9	1		10
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4	5		9
Total	0	1	13	8	1

Variants in ZRSR2

This is a list of pathogenic ClinVar variants found in the ZRSR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-15799901-A-G		not specified	Likely benign (Jun 24, 2022)
X-15803767-G-A		not specified	not provided (Sep 19, 2013)
X-15804153-A-G		not specified	Uncertain significance (Dec 06, 2022)
X-15808251-C-T			Likely benign (Oct 01, 2023)
X-15809200-T-C		not specified	Likely benign (Nov 21, 2023)
X-15809306-G-A		not specified	Uncertain significance (Dec 28, 2023)
X-15815829-T-A		not specified	Uncertain significance (Dec 17, 2023)
X-15815867-G-A		not specified	not provided (Sep 19, 2013)
X-15820288-C-T			Benign (Oct 24, 2017)
X-15820309-G-T			Likely benign (Sep 01, 2022)
X-15822802-A-G		not specified	Uncertain significance (Mar 25, 2022)
X-15822863-T-C		not specified	Uncertain significance (Jul 21, 2021)
X-15822903-C-G		not specified	Uncertain significance (Jan 06, 2023)
X-15822994-C-T		not specified	Uncertain significance (Jul 09, 2021)
X-15822999-CAG-C		Heart, malformation of;Median cleft lip and palate;Severe hydrocephalus;Holoprosencephaly sequence	Likely pathogenic (Oct 16, 2019)
X-15823063-G-C		not specified	Uncertain significance (Aug 23, 2021)
X-15823079-G-A		not specified	Uncertain significance (Jan 26, 2023)
X-15823090-C-T		not specified	Uncertain significance (Apr 25, 2023)
X-15823096-CG-AT		not specified	not provided (Sep 19, 2013)
X-15823100-G-A		not specified	not provided (Sep 19, 2013)
X-15823135-C-T		not specified	Uncertain significance (Aug 17, 2022)
X-15827084-T-G		Pettigrew syndrome	Uncertain significance (May 02, 2023)
X-15827324-G-A		Inborn genetic diseases	Uncertain significance (Jan 26, 2017)
X-15827326-T-C			Likely benign (Jul 25, 2023)
X-15827328-T-C			Likely benign (Nov 19, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZRSR2	protein_coding	protein_coding	ENST00000307771	11	32789

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000369	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.46	137	194	0.706	0.0000168	3199
Missense in Polyphen		17	50.836	0.33441		845
Synonymous	0.276	64	66.9	0.957	0.00000526	820
Loss of Function	4.41	0	22.7	0.00	0.00000191	356

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Pre-mRNA-binding protein required for splicing of both U2- and U12-type introns. Selectively interacts with the 3'-splice site of U2- and U12-type pre-mRNAs and promotes different steps in U2 and U12 intron splicing. Recruited to U12 pre-mRNAs in an ATP- dependent manner and is required for assembly of the prespliceosome, a precursor to other spliceosomal complexes. For U2-type introns, it is selectively and specifically required for the second step of splicing. {ECO:0000269|PubMed:21041408, ECO:0000269|PubMed:9237760}.
• Pathway: Metabolism of RNA;mRNA Splicing - Minor Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.95

Haploinsufficiency Scores

• pHI: 0.0612
• hipred: N
• hipred_score: 0.302
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.144

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zrsr2

Gene ontology

• Biological process: spliceosomal complex assembly;mRNA splicing, via spliceosome;RNA splicing
• Cellular component: nucleoplasm;spliceosomal complex;U12-type spliceosomal complex;U2AF
• Molecular function: protein binding;pre-mRNA 3'-splice site binding;metal ion binding