MIA2

protein-coding

MIA SH3 domain ER export factor 2, the group of CTAGE family|MIA family

Gene summary

This gene encodes s receptor in the endoplasmic reticulum, which plays a role in the export of large pre-chylomicrons and pre-very low density lipoproteins (pre-VLDLs). Three major classes of transcripts are generated from this gene- melanoma inhibitory activity 2-specific transcripts, cTAGE family member 5-specific transcripts and transcripts that include exons from both these transcript species (TANGO1-like or TALI). Additionally, alternative splicing in these transcripts results in multiple transcript variants encoding multiple isoforms. [provided by RefSeq, Sep 2016]

Previous symbols:

CTAGE5
MGEA
MGEA6

MANE transcript

NM_001329214.4

Inheritance

—

ClinVar variants

U:236B:21

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.39

Max pathogenic AF

—

Genomic locus

chr14:39,230,231-39,388,513

External References & Databases

Ensembl (ENSG00000150527)

Transcript & Mutation Effects

hg38 • Region Span ~158.3 kb

Loading mutation effect viewer...

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 MIA2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 236

not providedTotal: 12

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001329214.4. 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			4 clinvar	4 clinvar		8
missense			225 clinvar	16 clinvar	1 clinvar	242
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	236	20	1	257

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 92 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001329214.4	RefSeq	NP_001316143.1	29	MANE Select
ENST00000640607.2	Ensembl	ENSP00000491014.1	29	MANE Select
NM_001247988.1	RefSeq	NP_001234917.1	22	Standard
NM_001247989.2	RefSeq	NP_001234918.1	24	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000396158
Coding exons: 24
Length: 121669
Individuals with no LoFs: 125711
Homozygous LoFs: 0
Heterozygous LoFs: 37
Defined: 125748
p: 0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.877	447	398	1.12	0.0000188	5261
Missense (PolyPhen)		46	55.699	0.82587		825
Synonymous	-1.69	159	134	1.19	0.00000629	1467
Loss of Function	3.92	19	48.5	0.392	0.00000240	634

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.000055	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00016	0.00016	rare
South Asian	0.00017	0.00016	rare
Other	0.00016	0.00016	rare