TMIGD3

transmembrane and immunoglobulin domain containing 3

Basic information

Region (hg38): 1:111483348-111563962

Links

ENSG00000121933 ∙ NCBI:57413 ∙ ∙ HGNC:51375 ∙ Uniprot:P0DMS9 ∙ 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 TMIGD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMIGD3 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3	1	1	5
Total	0	0	8	1	1

Variants in TMIGD3

This is a list of pathogenic ClinVar variants found in the TMIGD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-111483740-G-C		not specified	Uncertain significance (Aug 12, 2021)
1-111486604-C-G		not specified	Uncertain significance (Aug 17, 2021)
1-111488688-CA-C		Autism	Uncertain significance (-)
1-111488767-G-A		not specified	Uncertain significance (Oct 12, 2021)
1-111490662-T-C		not specified	Uncertain significance (Oct 21, 2021)
1-111490694-A-G		not specified	Uncertain significance (Aug 02, 2021)
1-111500226-C-A		not specified	Uncertain significance (Nov 12, 2021)
1-111500290-T-A		not specified	Uncertain significance (Aug 12, 2021)
1-111500324-C-T		ADORA3-related disorder	Likely benign (May 22, 2023)
1-111500341-G-T		ADORA3-related disorder	Uncertain significance (Nov 08, 2023)
1-111503935-C-T			Benign (Aug 22, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMIGD3	protein_coding	protein_coding	ENST00000369716	6	80615

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000144	0.873	125697	0	51	125748	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.208	210	202	1.04	0.0000110	2278
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000367	0.000363
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000203	0.000202
Middle Eastern	0.000109	0.000109
South Asian	0.000426	0.000425
Other	0.000163	0.000163

dbNSFP

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}.
• Pathway: 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;GPCR signaling-G alpha i (Consensus)

Haploinsufficiency Scores

• pHI: 0.101
• ghis: 0.379

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Tmigd3
• Phenotype: hematopoietic system phenotype; cellular phenotype

Gene ontology

• Biological process: inflammatory response;signal transduction;activation of adenylate cyclase activity;regulation of heart contraction;negative regulation of cell population proliferation;response to wounding;negative regulation of cell migration;negative regulation of NF-kappaB transcription factor activity
• Cellular component: integral component of plasma membrane;membrane