MXRA5

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

Basic information

Region (hg38): X:3308564-3346652

Links

ENSG00000101825 ∙ NCBI:25878 ∙ OMIM:300938 ∙ HGNC:7539 ∙ Uniprot:Q9NR99 ∙ 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 MXRA5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MXRA5 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				10	14	24
missense			148	14	13	175
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding						0
Total	0	0	148	24	27

Variants in MXRA5

This is a list of pathogenic ClinVar variants found in the MXRA5 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-3309826-C-G		not specified	Uncertain significance (Apr 20, 2024)
X-3309969-G-A		not specified	Uncertain significance (Jan 03, 2024)
X-3309982-G-C		not specified	Uncertain significance (Feb 16, 2023)
X-3309988-G-A		not specified	Uncertain significance (Mar 08, 2024)
X-3310051-C-A		not specified	Uncertain significance (Mar 20, 2024)
X-3310179-T-C			Likely benign (Nov 01, 2022)
X-3310200-CGTCCCTGCCCAGCCCCG-TGTCCCTGCCCAGCTGCA			not provided (-)
X-3310282-T-C		not specified	Uncertain significance (Dec 20, 2023)
X-3310311-A-C		not specified	Uncertain significance (Sep 06, 2022)
X-3310337-A-C			Benign (Jan 04, 2022)
X-3310337-A-T			Benign (Mar 29, 2018)
X-3310348-G-A		not specified	Uncertain significance (Jun 06, 2023)
X-3310354-C-T		not specified	Uncertain significance (Aug 21, 2023)
X-3310360-G-A		not specified	Conflicting classifications of pathogenicity (Aug 02, 2023)
X-3310368-C-G			Uncertain significance (Sep 22, 2023)
X-3310370-G-A			Benign (Jan 29, 2022)
X-3310390-C-T			Benign (Apr 16, 2018)
X-3310439-C-A		not specified	Uncertain significance (May 30, 2023)
X-3310456-C-A		not specified	Uncertain significance (Jan 22, 2024)
X-3310464-T-C		not specified	Uncertain significance (Jul 12, 2023)
X-3310503-G-A		not specified	Uncertain significance (Jul 06, 2021)
X-3310535-C-T			Likely benign (Apr 01, 2023)
X-3310563-G-A		not specified	Uncertain significance (Aug 02, 2022)
X-3310612-G-C			Benign (May 20, 2020)
X-3310622-G-C			Benign (May 20, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MXRA5	protein_coding	protein_coding	ENST00000217939	6	38077

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0430	0.957	125710	17	21	125748	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.728	1213	1.14e+3	1.06	0.0000928	18435
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000680	0.000592
Ashkenazi Jewish	0.00134	0.000993
East Asian	0.000146	0.000109
Finnish	0.000126	0.0000924
European (Non-Finnish)	0.0000993	0.0000703
Middle Eastern	0.000146	0.000109
South Asian	0.000216	0.000131
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.226
• hipred: N
• hipred_score: 0.384
• ghis: 0.428

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.135

Gene Damage Prediction

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

Gene ontology

• Biological process: response to transforming growth factor beta
• Cellular component: collagen-containing extracellular matrix;extracellular exosome
• Molecular function: extracellular matrix structural constituent