MGARP

mitochondria localized glutamic acid rich protein

Basic information

Region (hg38): 4:139266165-139280225

Previous symbols: [ "C4orf49" ]

Links

ENSG00000137463 ∙ NCBI:84709 ∙ OMIM:619684 ∙ HGNC:29969 ∙ Uniprot:Q8TDB4 ∙ 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 MGARP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MGARP 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						0
missense			10	3		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	3	0

Variants in MGARP

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

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

Position	Type	Phenotype	Significance	ClinVar
4-139266612-G-A		not specified	Uncertain significance (Mar 15, 2024)
4-139266756-G-A		not specified	Uncertain significance (Dec 14, 2022)
4-139266790-C-T		not specified	Uncertain significance (Nov 16, 2021)
4-139266793-G-A		not specified	Likely benign (Jul 13, 2022)
4-139266795-G-A		not specified	Uncertain significance (Jul 12, 2023)
4-139266922-T-C		not specified	Likely benign (Nov 10, 2022)
4-139266961-C-T		not specified	Uncertain significance (May 14, 2024)
4-139267009-C-A		not specified	Uncertain significance (Oct 06, 2022)
4-139267033-C-T		not specified	Uncertain significance (Sep 20, 2023)
4-139268684-G-C		not specified	Uncertain significance (Feb 27, 2023)
4-139268742-G-T		not specified	Likely benign (Feb 17, 2022)
4-139275302-G-A		not specified	Uncertain significance (Sep 06, 2022)
4-139275315-C-T		not specified	Uncertain significance (Feb 28, 2024)
4-139275384-G-A		not specified	Uncertain significance (Oct 16, 2023)
4-139280103-G-A		not specified	Uncertain significance (Aug 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MGARP	protein_coding	protein_coding	ENST00000398955	4	14176

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000388	0.228	124769	0	12	124781	0.0000481

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.233	124	132	0.943	0.00000657	1526
Missense in Polyphen		29	29.135	0.99538		341
Synonymous	-0.233	55	52.8	1.04	0.00000293	507
Loss of Function	-0.508	6	4.80	1.25	2.00e-7	67

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000646	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000567	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000907	0.0000795
Middle Eastern	0.0000567	0.0000556
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the trafficking of mitochondria along microtubules. Regulates the kinesin-mediated axonal transport of mitochondria to nerve terminals along microtubules during hypoxia. Participates in the translocation of TRAK2/GRIF1 from the cytoplasm to the mitochondrion. Also plays a role in steroidogenesis through maintenance of mitochondrial abundance and morphology (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0831

Intolerance Scores

• rvis_EVS: 0.71
• rvis_percentile_EVS: 85.53

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mgarp

Gene ontology

• Biological process: protein targeting to mitochondrion;anterograde axonal transport;retrograde axonal transport;positive regulation of mitochondrion organization;axonal transport of mitochondrion;cellular response to steroid hormone stimulus;cellular response to hypoxia;cellular response to gonadotropin-releasing hormone
• Cellular component: mitochondrion;integral component of mitochondrial outer membrane;axon cytoplasm
• Molecular function: protein binding