MIGA1

mitoguardin 1

Basic information

Region (hg38): 1:77779624-77879540

Previous symbols: [ "FAM73A" ]

Links

ENSG00000180488 ∙ NCBI:374986 ∙ OMIM:616773 ∙ HGNC:24741 ∙ Uniprot:Q8NAN2 ∙ 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 MIGA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MIGA1 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	7	0	0

Variants in MIGA1

This is a list of pathogenic ClinVar variants found in the MIGA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-77779687-G-C		not specified	Uncertain significance (Sep 17, 2021)
1-77801478-G-C		not specified	Uncertain significance (Jun 11, 2021)
1-77803275-A-G		not specified	Uncertain significance (Jul 06, 2021)
1-77813737-T-C		not specified	Uncertain significance (Sep 16, 2021)
1-77861307-A-C		not specified	Uncertain significance (Nov 09, 2021)
1-77873037-A-G		not specified	Uncertain significance (Oct 06, 2021)
1-77874855-C-A		not specified	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MIGA1	protein_coding	protein_coding	ENST00000370791	16	98798

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.83e-7	0.999	125703	0	45	125748	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.532	302	329	0.917	0.0000165	4145
Missense in Polyphen		100	122.35	0.81731		1599
Synonymous	0.366	110	115	0.957	0.00000585	1165
Loss of Function	2.82	17	35.0	0.485	0.00000176	438

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000558	0.000558
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000181	0.000176
Middle Eastern	0.000163	0.000163
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulator of mitochondrial fusion: acts by forming homo- and heterodimers at the mitochondrial outer membrane and facilitating the formation of PLD6/MitoPLD dimers. May act by regulating phospholipid metabolism via PLD6/MitoPLD. {ECO:0000269|PubMed:26711011}.
• Pathway: Metabolism of lipids;Metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism;Synthesis of PA (Consensus)

Intolerance Scores

• rvis_EVS: -0.73
• rvis_percentile_EVS: 14.08

Haploinsufficiency Scores

• pHI: 0.342
• hipred: N
• hipred_score: 0.426
• ghis: 0.644

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Miga1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; vision/eye phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: mitochondrial fusion
• Cellular component: mitochondrial outer membrane;integral component of plasma membrane
• Molecular function: protein binding;protein homodimerization activity;protein heterodimerization activity