TMIGD3

protein-coding

transmembrane and immunoglobulin domain containing 3

Gene summary

This gene encodes a transmembrane and immunoglobulin domain-containing protein. Alternative splicing results in multiple transcript variants, one of which shares its 5' terminal exon with that of the overlapping adenosine A3 receptor gene (GeneID:140), thus resulting in a fusion product. [provided by RefSeq, Nov 2014]

MANE transcript

NM_020683.7

Inheritance

—

ClinVar variants

U:9

Top phenotype

ADORA3-related disorder

gnomAD constraint

pLI —, LoF o/e 0.59

Max pathogenic AF

—

Genomic locus

chr1:111,483,348-111,563,962

External References & Databases

Ensembl (ENSG00000121933)

Transcript & Mutation Effects

hg38 • Region Span ~80.6 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 TMIGD3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 7

ADORA3-related disorderTotal: 3

AutismTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020683.7. 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			1 clinvar			1
missense			7 clinvar			7
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	9	0	0	9

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020683.7	RefSeq	NP_065734.5	6	MANE Select
ENST00000369716.9	Ensembl	ENSP00000358730.4	6	MANE Select
NM_001081976.3	RefSeq	NP_001075445.1	6	Standard
NM_001302680.2	RefSeq	NP_001289609.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

GPCR signaling-G alpha q
GPCR signaling-cholera toxin
GPCR signaling-pertussis toxin
GPCR signaling-G alpha s Epac and ERK
GPCR signaling-G alpha s PKA and ERK

Biological Process

inflammatory response
signal transduction
activation of adenylate cyclase activity
regulation of heart contraction
negative regulation of cell population proliferation

Cellular Component

integral component of plasma membrane
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000369716
Coding exons: 6
Length: 80615
Individuals with no LoFs: 125697
Homozygous LoFs: 0
Heterozygous LoFs: 51
Defined: 125748
p: 0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.208	210	202	1.04	0.0000110	2278
Missense (PolyPhen)		70	67.92	1.0306		822
Synonymous	0.216	75	77.4	0.969	0.00000440	703
Loss of Function	1.39	8	13.5	0.591	7.45e-7	149

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	0.00011	0.00011	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00020	0.00020	rare
South Asian	0.00043	0.00042	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Isoform 1: Plays a suppressive role in osteosarcoma malignancy by inhibiting NF-kappa-B activity (PubMed:27886186). {ECO:0000269|PubMed:27886186}.;

Essentials

Essential (gene trap): N