CSRP2

cysteine and glycine rich protein 2, the group of LIM domain containing

Basic information

Region (hg38): 12:76858709-76879023

Links

ENSG00000175183 ∙ NCBI:1466 ∙ OMIM:601871 ∙ HGNC:2470 ∙ Uniprot:Q16527 ∙ 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 CSRP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSRP2 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in CSRP2

This is a list of pathogenic ClinVar variants found in the CSRP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-76858986-C-T		not specified	Uncertain significance (Oct 24, 2023)
12-76859616-A-G		not specified	Uncertain significance (Oct 07, 2024)
12-76859639-G-A		not specified	Uncertain significance (Dec 13, 2023)
12-76860344-C-G		not specified	Uncertain significance (Jun 14, 2024)
12-76863182-G-A		not specified	Uncertain significance (Dec 15, 2023)
12-76863206-C-T		not specified	Uncertain significance (May 03, 2023)
12-76863215-T-G		not specified	Uncertain significance (Mar 13, 2023)
12-76863288-A-G		not specified	Uncertain significance (Jan 23, 2024)
12-76863297-C-T		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSRP2	protein_coding	protein_coding	ENST00000311083	5	20346

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.77e-7	0.234	125715	0	31	125746	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.291	102	111	0.922	0.00000585	1262
Missense in Polyphen		25	30.5	0.81967		359
Synonymous	-0.239	43	41.1	1.05	0.00000249	358
Loss of Function	0.171	10	10.6	0.943	5.28e-7	137

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000445	0.000440
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.00	0.00
South Asian	0.000164	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Drastically down-regulated in response to PDGF-BB or cell injury, that promote smooth muscle cell proliferation and dedifferentiation. Seems to play a role in the development of the embryonic vascular system.
• Pathway: Mesodermal Commitment Pathway;H19 action Rb-E2F1 signaling and CDK-β-catenin activity;ATF-2 transcription factor network (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.510
• rvis_EVS: -0.14
• rvis_percentile_EVS: 42.88

Haploinsufficiency Scores

• pHI: 0.429
• hipred: Y
• hipred_score: 0.635
• ghis: 0.570

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Csrp2
• 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; muscle phenotype

Gene ontology

• Biological process: multicellular organism development;cell differentiation
• Cellular component: nucleus;focal adhesion
• Molecular function: molecular_function;protein binding;metal ion binding