CSRNP1

cysteine and serine rich nuclear protein 1

Basic information

Region (hg38): 3:39141855-39154562

Previous symbols: [ "AXUD1" ]

Links

ENSG00000144655 ∙ NCBI:64651 ∙ OMIM:606458 ∙ HGNC:14300 ∙ Uniprot:Q96S65 ∙ 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 CSRNP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSRNP1 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			56	3		59
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	56	3	0

Variants in CSRNP1

This is a list of pathogenic ClinVar variants found in the CSRNP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-39143101-A-G		not specified	Uncertain significance (Aug 01, 2024)
3-39143135-C-G		not specified	Uncertain significance (Apr 08, 2024)
3-39143135-C-T		not specified	Uncertain significance (Sep 08, 2024)
3-39143140-G-A		not specified	Uncertain significance (Nov 03, 2023)
3-39143141-G-A		not specified	Uncertain significance (Apr 06, 2023)
3-39143214-G-T		not specified	Uncertain significance (Apr 06, 2023)
3-39143284-T-A		not specified	Uncertain significance (Aug 26, 2024)
3-39143393-G-A			Likely benign (May 03, 2020)
3-39143395-C-T		not specified	Uncertain significance (Jul 25, 2023)
3-39143473-G-A		not specified	Uncertain significance (Aug 30, 2021)
3-39143503-G-A		not specified	Uncertain significance (Dec 14, 2021)
3-39143543-T-G		not specified	Uncertain significance (Sep 06, 2022)
3-39143567-G-A		not specified	Uncertain significance (Dec 08, 2023)
3-39143585-C-A		not specified	Uncertain significance (May 23, 2023)
3-39143647-C-T		not specified	Uncertain significance (Nov 25, 2024)
3-39143648-G-A		not specified	Uncertain significance (Aug 17, 2021)
3-39143660-C-T		not specified	Uncertain significance (Feb 03, 2022)
3-39143668-A-T		not specified	Uncertain significance (Mar 25, 2024)
3-39143675-G-A		not specified	Uncertain significance (Jan 31, 2022)
3-39143675-G-C		not specified	Uncertain significance (Feb 07, 2023)
3-39143710-G-A		not specified	Uncertain significance (Jul 26, 2022)
3-39143761-G-C		not specified	Uncertain significance (Mar 21, 2023)
3-39143800-T-A		not specified	Uncertain significance (Dec 06, 2022)
3-39143801-C-T		not specified	Uncertain significance (Dec 06, 2022)
3-39143906-C-T		not specified	Uncertain significance (Jun 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSRNP1	protein_coding	protein_coding	ENST00000273153	4	12708

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.343	0.657	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.290	344	359	0.957	0.0000221	3841
Missense in Polyphen		113	129.03	0.87575		1397
Synonymous	0.462	133	140	0.950	0.00000786	1219
Loss of Function	2.98	4	17.4	0.229	0.00000107	188

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000333	0.000333
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to the consensus sequence 5'-AGAGTG-3' and has transcriptional activator activity (By similarity). May have a tumor-suppressor function. May play a role in apoptosis. {ECO:0000250, ECO:0000269|PubMed:11526492}.

Recessive Scores

• pRec: 0.0996

Intolerance Scores

• loftool: 0.498
• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.54

Haploinsufficiency Scores

• pHI: 0.232
• hipred: N
• hipred_score: 0.314
• ghis: 0.480

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.523

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Csrnp1
• 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); skeleton phenotype; digestive/alimentary phenotype; craniofacial phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: csrnp1a
• Affected structure: neutrophil
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: apoptotic process;post-embryonic development;positive regulation of transcription by RNA polymerase II;platelet-derived growth factor receptor signaling pathway;skeletal system morphogenesis;roof of mouth development;face morphogenesis
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;molecular_function;DNA-binding transcription factor activity;protein binding;sequence-specific DNA binding