XIRP2

xin actin binding repeat containing 2, the group of LIM domain containing

Basic information

Region (hg38): 2:166888479-167259753

Previous symbols: [ "CMYA3" ]

Links

ENSG00000163092 ∙ NCBI:129446 ∙ OMIM:609778 ∙ HGNC:14303 ∙ Uniprot:A4UGR9 ∙ 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 XIRP2 gene.

• Inborn genetic diseases (146 variants)
• not provided (90 variants)
• not specified (2 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the XIRP2 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				17	12	29
missense			128	38	29	195
nonsense					1	1
start loss			1			1
frameshift			1			1
inframe indel				1		1
splice donor/acceptor (+/-2bp)				1		1
splice region						0
non coding				1		1
Total	0	0	130	58	42

Variants in XIRP2

This is a list of pathogenic ClinVar variants found in the XIRP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-166903484-T-C		XIRP2-related disorder	Likely benign (Feb 22, 2019)
2-166903492-A-G		XIRP2-related disorder	Benign (Dec 31, 2019)
2-166903503-C-T		XIRP2-related disorder	Likely benign (Jan 01, 2023)
2-166903521-G-A			Benign (Dec 31, 2019)
2-166903553-G-T		not specified	Uncertain significance (Mar 14, 2023)
2-166903698-T-C		XIRP2-related disorder	Likely benign (Jun 26, 2019)
2-166903729-A-G		not specified	Uncertain significance (Apr 18, 2023)
2-166903739-A-C		not specified	Likely benign (May 24, 2023)
2-166903756-C-T		not specified	Uncertain significance (Apr 20, 2023)
2-166903764-A-T		not specified	Uncertain significance (Mar 16, 2022)
2-166903789-A-T		not specified	Uncertain significance (Jun 28, 2022)
2-166903800-G-T		not specified	Uncertain significance (Mar 20, 2023)
2-166903860-T-G		not specified	Uncertain significance (Jun 07, 2022)
2-166903871-C-T		not specified	Uncertain significance (Jul 05, 2023)
2-167135928-G-A		not specified	Uncertain significance (Jul 20, 2022)
2-167135961-G-A		XIRP2-related disorder	Likely benign (Jul 12, 2019)
2-167135964-G-T		not specified	Uncertain significance (Aug 16, 2021)
2-167135972-G-A		not specified	Benign (Mar 29, 2016)
2-167136019-T-G		not specified	Uncertain significance (May 25, 2022)
2-167184571-C-T		XIRP2-related disorder	Uncertain significance (Jan 12, 2024)
2-167184577-C-T		XIRP2-related disorder	Benign (Dec 31, 2019)
2-167184588-T-C		XIRP2-related disorder	Benign/Likely benign (Apr 01, 2019)
2-167184642-T-C		XIRP2-related disorder	Benign (Oct 31, 2019)
2-167210814-C-T			Likely benign (Aug 13, 2018)
2-167210841-G-A		not specified	Uncertain significance (May 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
XIRP2	protein_coding	protein_coding	ENST00000409195	9	371267

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.08e-52	0.000783	123536	2	1267	124805	0.00510

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.40	2073	1.79e+3	1.16	0.0000900	23549
Missense in Polyphen		631	558.54	1.1297		7866
Synonymous	-1.68	692	638	1.08	0.0000335	6619
Loss of Function	2.22	95	121	0.783	0.00000627	1669

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0108	0.0107
Ashkenazi Jewish	0.000797	0.000795
East Asian	0.0124	0.0124
Finnish	0.00107	0.00107
European (Non-Finnish)	0.00517	0.00513
Middle Eastern	0.0124	0.0124
South Asian	0.00459	0.00455
Other	0.00365	0.00363

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protects actin filaments from depolymerization. {ECO:0000269|PubMed:15454575}.

Recessive Scores

• pRec: 0.0864

Intolerance Scores

• loftool: 0.976
• rvis_EVS: 1.46
• rvis_percentile_EVS: 95.19

Haploinsufficiency Scores

• pHI: 0.186
• hipred: N
• hipred_score: 0.146
• ghis: 0.454

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.615

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Xirp2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; normal 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); 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); muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: ventricular septum development;biological_process;actin cytoskeleton organization;cell-cell junction organization;cardiac muscle tissue morphogenesis
• Cellular component: stress fiber;focal adhesion;Z disc
• Molecular function: actin filament binding;alpha-actinin binding