MXRA5

protein-coding

matrix remodeling associated 5, the group of I-set domain containing

Gene summary

This gene encodes one of the matrix-remodelling associated proteins. This protein contains 7 leucine-rich repeats and 12 immunoglobulin-like C2-type domains related to perlecan. This gene has a pseudogene on chromosome Y. [provided by RefSeq, Mar 2010]

MANE transcript

NM_015419.4

Inheritance

—

ClinVar variants

U:569B:58

Top phenotype

Short stature

gnomAD constraint

pLI —, LoF o/e 0.25

Max pathogenic AF

—

Genomic locus

chrX:3,308,565-3,346,652

External References & Databases

Ensembl (ENSG00000101825)

Transcript & Mutation Effects

hg38 • Region Span ~38.1 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 MXRA5 variants in ClinVar

6 Conditions Cataloged

not specifiedTotal: 380

not providedTotal: 53

Short statureTotal: 2

Prostate cancerTotal: 1

MXRA5-related disorderTotal: 1

Nephrotic syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015419.4. 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			55 clinvar	10 clinvar	9 clinvar	74
missense			481 clinvar	29 clinvar	10 clinvar	520
nonsense			25 clinvar			25
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	569	39	19	627

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015419.4	RefSeq	NP_056234.2	6	MANE Select
ENST00000217939.7	Ensembl	ENSP00000217939.5	6	MANE Select
ENST00001036904.1	Ensembl	ENSP00000706721.1	2	Standard
ENST00001135270.1	Ensembl	ENSP00000801608.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

response to transforming growth factor beta

Molecular Function

extracellular matrix structural constituent

Cellular Component

collagen-containing extracellular matrix
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000217939
Coding exons: 6
Length: 38077
Individuals with no LoFs: 125710
Homozygous LoFs: 17
Heterozygous LoFs: 21
Defined: 125748
p: 0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.728	1213	1.14e+3	1.06	0.0000928	18435
Missense (PolyPhen)		359	375.13	0.957		5770
Synonymous	-0.195	481	476	1.01	0.0000424	5876
Loss of Function	5.12	14	55.0	0.255	0.00000413	996

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00046	0.00037	rare
Latino/Admixed American	0.00022	0.00017	rare
Ashkenazi Jewish	0.0013	0.00099	notable
East Asian	0.00015	0.00011	rare
Finnish	0.00013	0.000092	rare
European (Non-Finnish)	0.000099	0.000070	rare
South Asian	0.00022	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: In kidney, has anti-inflammatory and anti-fibrotic properties by limiting the induction of chemokines, fibronectin and collagen expression in response to TGB1 and pro-inflammatory stimuli. {ECO:0000269|PubMed:27599751}.;
Disease: DISEASE: Lung cancer (LNCR) [MIM:211980]: A common malignancy affecting tissues of the lung. The most common form of lung cancer is non-small cell lung cancer (NSCLC) that can be divided into 3 major histologic subtypes: squamous cell carcinoma, adenocarcinoma, and large cell lung cancer. NSCLC is often diagnosed at an advanced stage and has a poor prognosis. {ECO:0000269|PubMed:22696596}. Note=Disease susceptibility may be associated with variations affecting the gene represented in this entry.;

Recessive Scores

pRec: 0.0949

Intolerance Scores

LoFtool: 0.310
RVIS EVS: 1.57
RVIS percentile EVS: 95.68

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.135

Gene Damage Prediction

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