XIRP1

xin actin binding repeat containing 1

Basic information

Region (hg38): 3:39183210-39192596

Previous symbols: [ "CMYA1" ]

Links

ENSG00000168334 ∙ NCBI:165904 ∙ OMIM:609777 ∙ HGNC:14301 ∙ Uniprot:Q702N8 ∙ 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 XIRP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the XIRP1 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				13	13	26
missense			139	22	27	188
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	1	2
Total	0	0	139	37	41

Variants in XIRP1

This is a list of pathogenic ClinVar variants found in the XIRP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-39183910-G-A		XIRP1-related disorder	Benign (Jun 18, 2019)
3-39183954-A-G		not specified	Likely benign (Jan 03, 2024)
3-39183957-G-A		XIRP1-related disorder	Likely benign (Feb 21, 2023)
3-39183969-G-A		not specified	Uncertain significance (Aug 22, 2023)
3-39183987-C-T		not specified	Uncertain significance (Sep 01, 2021)
3-39184011-C-A		not specified	Uncertain significance (Aug 28, 2023)
3-39184031-G-C		XIRP1-related disorder	Benign (Dec 31, 2019)
3-39184050-G-A		not specified	Uncertain significance (Mar 29, 2024)
3-39184051-G-A		not specified	Uncertain significance (Dec 12, 2023)
3-39184058-G-C		XIRP1-related disorder	Benign (Dec 31, 2019)
3-39184075-C-T		not specified	Uncertain significance (May 11, 2022)
3-39184094-C-T		XIRP1-related disorder	Benign (Jan 01, 2023)
3-39184144-C-T		XIRP1-related disorder	Benign (May 27, 2019)
3-39184159-C-T		not specified	Uncertain significance (Nov 15, 2021)
3-39184168-G-T		not specified	Uncertain significance (Jan 16, 2024)
3-39184185-G-A		not specified	Uncertain significance (Aug 13, 2021)
3-39184228-G-T		not specified	Uncertain significance (Sep 26, 2023)
3-39184255-G-A		not specified	Uncertain significance (Nov 27, 2023)
3-39184261-C-G		XIRP1-related disorder	Benign (Nov 06, 2019)
3-39184267-A-G		not specified	Uncertain significance (Aug 10, 2021)
3-39184268-C-G		not specified	Uncertain significance (Apr 20, 2023)
3-39184276-T-C		XIRP1-related disorder	Benign (Dec 31, 2019)
3-39184302-A-T		not specified	Uncertain significance (Apr 09, 2024)
3-39184325-C-A		XIRP1-related disorder	Benign (Dec 31, 2019)
3-39184344-A-G		XIRP1-related disorder	Likely benign (Mar 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
XIRP1	protein_coding	protein_coding	ENST00000340369	1	9387

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.27e-30	0.000313	125412	1	335	125748	0.00134

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.348	1080	1.05e+3	1.03	0.0000603	11865
Missense in Polyphen		254	267.04	0.95115		3000
Synonymous	-1.43	472	434	1.09	0.0000253	3996
Loss of Function	0.547	48	52.3	0.918	0.00000304	536

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00390	0.00390
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00120	0.00120
Finnish	0.000187	0.000185
European (Non-Finnish)	0.00110	0.00107
Middle Eastern	0.00120	0.00120
South Asian	0.00177	0.00170
Other	0.00229	0.00228

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.188

Intolerance Scores

• loftool: 0.871
• rvis_EVS: 1.64
• rvis_percentile_EVS: 96.09

Haploinsufficiency Scores

• pHI: 0.0944
• hipred: N
• hipred_score: 0.146
• ghis: 0.384

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.140

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Xirp1
• Phenotype: growth/size/body region phenotype; muscle 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)

Gene ontology

• Biological process: actin filament organization;heart development;negative regulation of protein binding
• Cellular component: stress fiber;focal adhesion
• Molecular function: RNA binding;protein binding;actin filament binding