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

ENSG00000178662NCBI:80034HGNC:30729Uniprot:Q8WYN3AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CSRNP3 gene.

  • not_specified (64 variants)
  • not_provided (3 variants)

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. These statistics are base on transcript: NM_001172173.2. 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
2
clinvar
3
missense
64
clinvar
64
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 64 1 2
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CSRNP3protein_codingprotein_codingENST00000314499 4219761
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.5000.5001257360101257460.0000398
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.592483290.7540.00001873875
Missense in Polyphen90158.850.566561901
Synonymous-0.2271331301.030.000008161123
Loss of Function3.55523.60.2120.00000177255

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001200.000120
Ashkenazi Jewish0.000.00
East Asian0.00005450.0000544
Finnish0.000.00
European (Non-Finnish)0.00005310.0000527
Middle Eastern0.00005450.0000544
South Asian0.000.00
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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