MIA

MIA SH3 domain containing, the group of MIA family

Basic information

Region (hg38): 19:40771647-40777490

Links

ENSG00000261857 ∙ NCBI:8190 ∙ OMIM:601340 ∙ HGNC:7076 ∙ Uniprot:Q16674 ∙ 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 MIA gene.

• Inborn genetic diseases (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MIA 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	1		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	6	1	0

Variants in MIA

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

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

Position	Type	Phenotype	Significance	ClinVar
19-40775513-CCTTGCTCACTCT-C		MIA-related disorder	Likely benign (Aug 29, 2019)
19-40775549-C-T		not specified	Likely benign (Nov 09, 2021)
19-40775577-T-C		not specified	Uncertain significance (Sep 29, 2022)
19-40775652-C-T		MIA-related disorder	Benign (Oct 14, 2019)
19-40775832-G-C		not specified	Uncertain significance (Oct 27, 2023)
19-40775839-T-C		not specified	Uncertain significance (Dec 13, 2022)
19-40775859-C-T		not specified	Uncertain significance (Jan 18, 2023)
19-40775878-G-C		not specified	Uncertain significance (Jun 02, 2023)
19-40776985-A-G		not specified	Uncertain significance (Dec 05, 2022)
19-40777403-G-T		not specified	Uncertain significance (Oct 04, 2022)
19-40777424-C-T		MIA-related disorder	Likely benign (Jul 09, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MIA	protein_coding	protein_coding	ENST00000263369	4	5843

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000173	0.456	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.532	70	83.7	0.836	0.00000509	836
Missense in Polyphen		38	39.409	0.96426		389
Synonymous	0.512	27	30.6	0.882	0.00000154	276
Loss of Function	0.482	8	9.61	0.832	8.17e-7	69

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000334	0.000333
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.000272	0.000272
South Asian	0.0000984	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Elicits growth inhibition on melanoma cells in vitro as well as some other neuroectodermal tumors, including gliomas.
• Pathway: Neural Crest Differentiation (Consensus)

Recessive Scores

• pRec: 0.0863

Intolerance Scores

• loftool: 0.643
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.33

Haploinsufficiency Scores

• pHI: 0.0973
• hipred: N
• hipred_score: 0.112
• ghis: 0.508

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.929

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mia
• Phenotype: skeleton phenotype

Gene ontology

• Biological process: cell population proliferation;regulation of signaling receptor activity
• Cellular component: extracellular space
• Molecular function: growth factor activity