XIRP1

protein-coding

xin actin binding repeat containing 1

Gene summary

The protein encoded by this gene is a striated muscle protein and belongs to the Xin actin-binding repeat-containing protein (XIRP) family. The protein functions to protect actin filaments during depolymerization. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2017]

Previous symbols:

CMYA1

MANE transcript

NM_194293.4

Inheritance

—

ClinVar variants

U:323B:78

Top phenotype

XIRP1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.92

Max pathogenic AF

—

Genomic locus

chr3:39,183,210-39,192,596

External References & Databases

Ensembl (ENSG00000168334)

Transcript & Mutation Effects

hg38 • Region Span ~9.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to XIRP1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 331

XIRP1-related disorderTotal: 58

not providedTotal: 38

Classical primary microcephalyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_194293.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	14 clinvar	12 clinvar	29
missense			319 clinvar	28 clinvar	23 clinvar	370
nonsense				1 clinvar		1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	323	43	35	401

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_194293.4	RefSeq	NP_919269.2	1	MANE Select
ENST00000340369.4	Ensembl	ENSP00000343140.3	1	MANE Select
NM_001198621.4	RefSeq	NP_001185550.1	2	Standard
NM_001351377.2	RefSeq	NP_001338306.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

actin filament organization
heart development
negative regulation of protein binding

Molecular Function

RNA binding
protein binding
actin filament binding

Cellular Component

stress fiber
focal adhesion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000340369
Coding exons: 1
Length: 9387
Individuals with no LoFs: 125412
Homozygous LoFs: 1
Heterozygous LoFs: 335
Defined: 125748
p: 0.00134

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.348	1080	1.05e+3	1.03	0.0000603	11865
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00080	0.00080	rare
Latino/Admixed American	0.0031	0.0031	notable
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.0012	0.0012	notable
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.0011	0.0011	notable
South Asian	0.0018	0.0017	notable
Other	0.0023	0.0023	notable

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.140

Gene Damage Prediction

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