MIA

protein-coding

MIA SH3 domain containing, the group of MIA family

Gene summary

Predicted to enable growth factor activity. Predicted to be involved in extracellular matrix organization. Predicted to act upstream of or within cell-matrix adhesion. Predicted to be located in obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_006533.4

Inheritance

—

ClinVar variants

U:15B:2

Top phenotype

MIA-related disorder

gnomAD constraint

pLI —, LoF o/e 0.83

Max pathogenic AF

—

Genomic locus

chr19:40,771,648-40,777,490

External References & Databases

Ensembl (ENSG00000261857)

Transcript & Mutation Effects

hg38 • Region Span ~5.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MIA variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 16

MIA-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006533.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			15 clinvar	1 clinvar	1 clinvar	17
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	15	1	1	17

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006533.4	RefSeq	NP_006524.1	4	MANE Select
ENST00000263369.4	Ensembl	ENSP00000263369.2	4	MANE Select
NM_001202553.2	RefSeq	NP_001189482.1	4	Standard
ENST00000594436.5	Ensembl	ENSP00000470129.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Neural Crest Differentiation

Biological Process

cell population proliferation
regulation of signaling receptor activity

Molecular Function

growth factor activity

Cellular Component

extracellular space

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000263369
Coding exons: 4
Length: 5843
Individuals with no LoFs: 125728
Homozygous LoFs: 0
Heterozygous LoFs: 20
Defined: 125748
p: 0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.532	70	83.7	0.836	0.00000509	836
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00027	0.00027	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Elicits growth inhibition on melanoma cells in vitro as well as some other neuroectodermal tumors, including gliomas.;

Recessive Scores

pRec: 0.0863

Intolerance Scores

LoFtool: 0.643
RVIS EVS: 0.17
RVIS percentile EVS: 65.33

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.929

Gene Damage Prediction

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