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:15790156-15830694

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.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Orofaciodigital syndrome XXI	XL	Endocrine	Early-onset endocrine abnormalities related to pituitary dysfunction have been described, and awareness may allow medical management	Craniofacial; Endocrine; Musculoskeletal; Neurologic	38158857

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZRSR2 gene.

• not_specified (33 variants)
• not_provided (12 variants)
• Orofaciodigital_syndrome_21 (2 variants)
• Severe_hydrocephalus (1 variants)
• Median_cleft_lip_and_palate (1 variants)
• Holoprosencephaly_sequence (1 variants)
• Heart,_malformation_of (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. These statistics are base on transcript: NM_000005089.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				5	1	6
missense			31	1		32
nonsense	1	1				2
start loss						0
frameshift	1	2				3
splice donor/acceptor (+/-2bp)						0
Total	2	3	31	6	1

Highest pathogenic variant AF is 9.105387e-7

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