CSRNP3

cysteine and serine rich nuclear protein 3, the group of Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 2:165469647-165689407

Previous symbols: [ "FAM130A2" ]

Links

ENSG00000178662 ∙ NCBI:80034 ∙ ∙ HGNC:30729 ∙ Uniprot:Q8WYN3 ∙ 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 CSRNP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSRNP3 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				1	2	3
missense			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	2

Variants in CSRNP3

This is a list of pathogenic ClinVar variants found in the CSRNP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-165595105-G-A		not specified	Uncertain significance (Jan 16, 2024)
2-165595123-T-C		not specified	Uncertain significance (Jun 28, 2023)
2-165657901-C-T		not specified	Uncertain significance (Jan 31, 2024)
2-165657913-G-A		not specified	Uncertain significance (Apr 08, 2024)
2-165676355-T-C		not specified	Uncertain significance (Mar 24, 2023)
2-165676396-A-G		not specified	Uncertain significance (Dec 06, 2022)
2-165676412-A-C		not specified	Uncertain significance (Aug 13, 2021)
2-165676591-G-A		not specified	Uncertain significance (May 05, 2023)
2-165678847-A-C		not specified	Uncertain significance (Dec 16, 2023)
2-165678881-A-G		not specified	Uncertain significance (Apr 27, 2023)
2-165678911-G-A		not specified	Uncertain significance (Oct 27, 2023)
2-165678950-A-G		not specified	Uncertain significance (Mar 01, 2023)
2-165678971-G-T		not specified	Uncertain significance (Apr 22, 2022)
2-165678992-G-T		not specified	Uncertain significance (Apr 24, 2024)
2-165679005-A-G		not specified	Uncertain significance (Apr 20, 2024)
2-165679036-G-C		not specified	Uncertain significance (Oct 25, 2023)
2-165679078-G-A			Benign (Feb 01, 2018)
2-165679159-C-T			Likely benign (Apr 01, 2022)
2-165679172-T-C		not specified	Uncertain significance (Nov 01, 2021)
2-165679182-G-A		not specified	Uncertain significance (Sep 14, 2022)
2-165679202-G-C		not specified	Uncertain significance (Jun 27, 2022)
2-165679205-G-T		not specified	Uncertain significance (Jan 10, 2023)
2-165679220-G-C		not specified	Uncertain significance (Mar 29, 2023)
2-165679221-T-G		not specified	Uncertain significance (Feb 28, 2024)
2-165679246-C-A			Benign (Aug 14, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSRNP3	protein_coding	protein_coding	ENST00000314499	4	219761

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.500	0.500	125736	0	10	125746	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.59	248	329	0.754	0.0000187	3875
Missense in Polyphen		90	158.85	0.56656		1901
Synonymous	-0.227	133	130	1.03	0.00000816	1123
Loss of Function	3.55	5	23.6	0.212	0.00000177	255

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000531	0.0000527
Middle Eastern	0.0000545	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.331
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.36

Haploinsufficiency Scores

• pHI: 0.827
• hipred: Y
• hipred_score: 0.768
• ghis: 0.622

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0531

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Csrnp3
• 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 apoptotic process;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;sequence-specific DNA binding