CSRNP2

cysteine and serine rich nuclear protein 2, the group of Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 12:51061205-51083664

Previous symbols: [ "C12orf22", "FAM130A1" ]

Links

ENSG00000110925 ∙ NCBI:81566 ∙ ∙ HGNC:16006 ∙ Uniprot:Q9H175 ∙ 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 CSRNP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSRNP2 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			34			34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	0	0

Variants in CSRNP2

This is a list of pathogenic ClinVar variants found in the CSRNP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-51063766-C-G		not specified	Uncertain significance (Oct 06, 2022)
12-51063810-G-T		not specified	Uncertain significance (Feb 01, 2023)
12-51063823-C-T		not specified	Uncertain significance (Sep 22, 2023)
12-51063846-C-T		not specified	Uncertain significance (Dec 21, 2022)
12-51063847-G-A		not specified	Uncertain significance (Jan 19, 2024)
12-51063856-G-C		not specified	Uncertain significance (Nov 12, 2021)
12-51063864-G-A		not specified	Uncertain significance (Jul 06, 2021)
12-51063885-T-A		not specified	Uncertain significance (Jul 09, 2021)
12-51063952-C-T		not specified	Uncertain significance (Nov 30, 2022)
12-51064054-A-T		not specified	Uncertain significance (Mar 25, 2024)
12-51064074-C-G		not specified	Uncertain significance (Sep 06, 2022)
12-51064090-C-T		not specified	Uncertain significance (Oct 06, 2021)
12-51064094-C-A		not specified	Uncertain significance (May 29, 2024)
12-51064142-C-G		not specified	Uncertain significance (Dec 19, 2023)
12-51064153-G-C		not specified	Uncertain significance (Nov 03, 2022)
12-51064164-G-A		not specified	Uncertain significance (Feb 23, 2023)
12-51064165-T-C		not specified	Likely benign (May 15, 2024)
12-51064233-T-C		not specified	Uncertain significance (Feb 10, 2022)
12-51064306-C-T		not specified	Uncertain significance (May 04, 2022)
12-51064318-C-T		not specified	Uncertain significance (Jul 15, 2021)
12-51064348-C-A		not specified	Uncertain significance (Apr 09, 2024)
12-51064510-G-C		not specified	Uncertain significance (Apr 12, 2024)
12-51064513-C-T		not specified	Uncertain significance (Apr 25, 2023)
12-51064533-C-T		not specified	Uncertain significance (Jan 19, 2024)
12-51064591-T-C		not specified	Uncertain significance (Dec 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSRNP2	protein_coding	protein_coding	ENST00000228515	4	22458

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.960	0.0398	125738	0	9	125747	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.17	214	324	0.660	0.0000193	3528
Missense in Polyphen		72	155.75	0.46227		1663
Synonymous	1.76	103	128	0.802	0.00000693	1130
Loss of Function	3.60	2	18.9	0.106	0.00000120	204

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to the consensus sequence 5'-AGAGTG-3' and has transcriptional activator activity (By similarity). May play a role in apoptosis. {ECO:0000250}.

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.431
• rvis_EVS: -0.25
• rvis_percentile_EVS: 36.07

Haploinsufficiency Scores

• pHI: 0.504
• hipred: Y
• hipred_score: 0.662
• ghis: 0.570

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.364

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Csrnp2
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: apoptotic process;negative regulation of phosphatase activity;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;phosphatase binding;sequence-specific DNA binding