CSRP1

cysteine and glycine rich protein 1, the group of LIM domain containing

Basic information

Region (hg38): 1:201483530-201509456

Previous symbols: [ "CYRP" ]

Links

ENSG00000159176 ∙ NCBI:1465 ∙ OMIM:123876 ∙ HGNC:2469 ∙ Uniprot:P21291 ∙ 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 CSRP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSRP1 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			18		1	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	3

Variants in CSRP1

This is a list of pathogenic ClinVar variants found in the CSRP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-201484762-T-A		not specified	Uncertain significance (Jul 07, 2024)
1-201485361-A-G		not specified	Uncertain significance (Nov 23, 2024)
1-201488879-C-T			Benign (Aug 16, 2018)
1-201488886-T-C		not specified	Uncertain significance (Aug 20, 2024)
1-201488887-A-G		not specified	Uncertain significance (Feb 13, 2024)
1-201488894-C-G		not specified	Uncertain significance (Mar 29, 2023)
1-201488904-C-T		not specified	Uncertain significance (May 24, 2023)
1-201488917-C-T		not specified	Uncertain significance (May 27, 2022)
1-201488934-T-A		not specified	Uncertain significance (May 23, 2023)
1-201488951-A-G			Likely benign (Oct 01, 2022)
1-201488961-G-A		not specified	Uncertain significance (Jan 05, 2022)
1-201490197-G-A		not specified	Uncertain significance (Sep 14, 2022)
1-201490237-C-T		not specified	Uncertain significance (Aug 16, 2022)
1-201490242-C-G		not specified	Uncertain significance (Aug 17, 2022)
1-201490248-C-A		not specified	Uncertain significance (Nov 03, 2023)
1-201490271-G-A			Benign (Aug 16, 2018)
1-201490306-C-T		not specified	Uncertain significance (Aug 17, 2021)
1-201496194-C-G		not specified	Uncertain significance (May 23, 2024)
1-201496222-T-C			Benign (Aug 09, 2018)
1-201496233-T-G		not specified	Uncertain significance (Jun 22, 2024)
1-201496257-G-A		not specified	Uncertain significance (Dec 01, 2022)
1-201496276-A-G		not specified	Uncertain significance (May 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSRP1	protein_coding	protein_coding	ENST00000367306	5	25927

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000333	0.833	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.215	107	113	0.943	0.00000613	1253
Missense in Polyphen		35	42.288	0.82766		471
Synonymous	0.510	43	47.5	0.906	0.00000295	365
Loss of Function	1.23	7	11.5	0.609	6.38e-7	131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000423	0.000423
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.000109	0.000109
South Asian	0.000196	0.000196
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Could play a role in neuronal development.
• Pathway: miR-targeted genes in adipocytes - TarBase;miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;MECP2 and Associated Rett Syndrome;MTF1 activates gene expression;MTF1 activates gene expression;Response to metal ions;Cellular responses to external stimuli (Consensus)

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.261
• rvis_EVS: 0.22
• rvis_percentile_EVS: 67.92

Haploinsufficiency Scores

• pHI: 0.282
• hipred: N
• hipred_score: 0.459
• ghis: 0.456

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.981

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Csrp1
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: csrp1a
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: platelet aggregation
• Cellular component: nucleus;focal adhesion;extracellular exosome
• Molecular function: RNA binding;zinc ion binding