MIX23

mitochondrial matrix import factor 23

Basic information

Region (hg38): 3:122359591-122383231

Previous symbols: [ "CCDC58" ]

Links

ENSG00000160124 ∙ NCBI:131076 ∙ ∙ HGNC:31136 ∙ Uniprot:Q4VC31 ∙ 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 MIX23 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MIX23 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in MIX23

This is a list of pathogenic ClinVar variants found in the MIX23 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-122359879-T-G		not specified	Uncertain significance (Nov 07, 2022)
3-122359900-C-T		not specified	Uncertain significance (Nov 14, 2023)
3-122359906-C-T		not specified	Uncertain significance (Nov 21, 2022)
3-122363019-C-G		not specified	Uncertain significance (Feb 12, 2024)
3-122371709-T-A		not specified	Uncertain significance (Apr 17, 2023)
3-122371762-T-C		not specified	Uncertain significance (Dec 06, 2021)
3-122383203-C-T		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MIX23	protein_coding	protein_coding	ENST00000291458	5	23641

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00406	0.870	125721	0	12	125733	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.896	53	74.8	0.708	0.00000360	949
Missense in Polyphen		10	16.665	0.60007		232
Synonymous	-0.544	31	27.4	1.13	0.00000150	245
Loss of Function	1.29	5	9.24	0.541	4.75e-7	110

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000919	0.0000919
Ashkenazi Jewish	0.00	0.00
East Asian	0.000119	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000443	0.0000440
Middle Eastern	0.000119	0.000109
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.623
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

• pHI: 0.592
• hipred: N
• hipred_score: 0.441
• ghis: 0.642

Essentials

• essential_gene_CRISPR: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.508

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc58