MICU3

mitochondrial calcium uptake family member 3, the group of EF-hand domain containing

Basic information

Region (hg38): 8:17027237-17122642

Previous symbols: [ "EFHA2" ]

Links

ENSG00000155970 ∙ NCBI:286097 ∙ OMIM:610633 ∙ HGNC:27820 ∙ Uniprot:Q86XE3 ∙ 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 MICU3 gene.

• Inborn genetic diseases (25 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MICU3 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			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	0

Variants in MICU3

This is a list of pathogenic ClinVar variants found in the MICU3 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-17027401-G-A		not specified	Uncertain significance (Dec 19, 2023)
8-17027433-G-A		not specified	Uncertain significance (Aug 05, 2022)
8-17027436-G-A		not specified	Uncertain significance (Jun 09, 2022)
8-17027471-G-C		not specified	Uncertain significance (Apr 13, 2022)
8-17027472-G-T		not specified	Uncertain significance (Dec 26, 2023)
8-17027475-G-C		not specified	Uncertain significance (Sep 01, 2021)
8-17027485-T-G		not specified	Uncertain significance (Jan 23, 2024)
8-17027538-G-C		not specified	Uncertain significance (Sep 06, 2022)
8-17027569-G-A		not specified	Uncertain significance (Jan 26, 2022)
8-17027613-C-A		not specified	Uncertain significance (Nov 17, 2022)
8-17027622-G-A		not specified	Uncertain significance (Nov 20, 2023)
8-17027649-G-A		not specified	Uncertain significance (Jul 19, 2022)
8-17027656-A-C		not specified	Uncertain significance (Mar 29, 2022)
8-17027657-G-C		not specified	Uncertain significance (Jul 15, 2021)
8-17064105-A-G		not specified	Uncertain significance (Dec 13, 2023)
8-17064106-T-C		not specified	Likely benign (Nov 18, 2023)
8-17064136-G-C		not specified	Uncertain significance (Dec 27, 2023)
8-17064196-C-T		not specified	Uncertain significance (Sep 07, 2022)
8-17077801-G-T		not specified	Likely benign (Apr 13, 2023)
8-17081693-G-A		not specified	Uncertain significance (Jun 03, 2022)
8-17085239-C-T		not specified	Uncertain significance (Feb 14, 2023)
8-17090559-A-G		not specified	Uncertain significance (Jun 05, 2023)
8-17098471-A-T		not specified	Uncertain significance (Feb 22, 2023)
8-17098498-A-G		not specified	Uncertain significance (Jun 06, 2023)
8-17098502-G-C		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MICU3	protein_coding	protein_coding	ENST00000318063	14	95407

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.40e-9	0.768	125678	0	57	125735	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.219	228	238	0.960	0.0000125	3406
Missense in Polyphen		38	55.922	0.67951		788
Synonymous	-1.80	99	78.7	1.26	0.00000383	993
Loss of Function	1.49	17	25.1	0.678	0.00000121	362

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000730	0.000729
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.000142	0.000139
European (Non-Finnish)	0.000266	0.000255
Middle Eastern	0.0000546	0.0000544
South Asian	0.0000328	0.0000327
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in mitochondrial calcium uptake. {ECO:0000250}.
• Pathway: Transport of small molecules;Mitochondrial calcium ion transport;Processing of SMDT1 (Consensus)

Intolerance Scores

• rvis_EVS: -0.74
• rvis_percentile_EVS: 13.94

Haploinsufficiency Scores

• pHI: 0.123
• hipred: N
• hipred_score: 0.291
• ghis: 0.621

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• 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: Micu3

Gene ontology

• Biological process: mitochondrial calcium ion transmembrane transport
• Cellular component: mitochondrial inner membrane;integral component of membrane
• Molecular function: calcium ion binding