TMIGD2

transmembrane and immunoglobulin domain containing 2, the group of Immunoglobulin like domain containing

Basic information

Region (hg38): 19:4292226-4302431

Links

ENSG00000167664 ∙ NCBI:126259 ∙ OMIM:614715 ∙ HGNC:28324 ∙ Uniprot:Q96BF3 ∙ 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 TMIGD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMIGD2 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					3	3
missense			12	5	3	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	5	6

Variants in TMIGD2

This is a list of pathogenic ClinVar variants found in the TMIGD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-4292624-C-G		not specified	Uncertain significance (Apr 17, 2023)
19-4292636-G-A		not specified	Uncertain significance (Mar 26, 2024)
19-4292679-A-C		not specified	Uncertain significance (Jun 24, 2022)
19-4292689-G-C			Benign (Dec 31, 2019)
19-4292691-C-T		not specified	Likely benign (Feb 05, 2024)
19-4292702-C-T		not specified	Uncertain significance (Apr 17, 2023)
19-4292736-A-G		not specified	Uncertain significance (Mar 01, 2023)
19-4292753-C-T		not specified	Uncertain significance (Mar 17, 2023)
19-4292754-G-T		not specified	Uncertain significance (Jan 04, 2024)
19-4292777-G-A		not specified	Likely benign (Jun 29, 2023)
19-4292814-C-G		not specified	Uncertain significance (Jan 29, 2024)
19-4292865-C-T		not specified	Uncertain significance (Apr 25, 2023)
19-4294602-C-T		not specified	Uncertain significance (Aug 17, 2021)
19-4294603-G-A		not specified	Uncertain significance (Jan 27, 2022)
19-4294647-A-G		not specified	Uncertain significance (Jun 17, 2024)
19-4294669-C-G		not specified	Uncertain significance (May 18, 2022)
19-4294669-C-T		not specified	Uncertain significance (Jun 03, 2024)
19-4298067-C-T			Benign (Dec 31, 2019)
19-4298078-T-C		not specified	Likely benign (Jun 29, 2022)
19-4298135-C-T		not specified	Likely benign (Jul 06, 2021)
19-4298201-G-A			Benign (Dec 31, 2019)
19-4298226-G-A		not specified	Uncertain significance (Jul 08, 2022)
19-4298231-C-T		not specified	Likely benign (Nov 07, 2022)
19-4298244-T-G			Benign (Dec 31, 2019)
19-4298248-C-T			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMIGD2	protein_coding	protein_coding	ENST00000301272	5	10200

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000109	0.369	125737	0	10	125747	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0953	169	173	0.980	0.0000105	1801
Missense in Polyphen		25	35.792	0.69849		337
Synonymous	-1.25	88	74.3	1.18	0.00000481	571
Loss of Function	0.291	8	8.94	0.895	3.85e-7	93

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000541	0.0000527
Middle Eastern	0.000167	0.000163
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in cell-cell interaction, cell migration, and angiogenesis. Through interaction with HHLA2, costimulates T- cells in the context of TCR-mediated activation. Enhances T-cell proliferation and cytokine production via an AKT-dependent signaling cascade. {ECO:0000269|PubMed:22419821, ECO:0000269|PubMed:23784006}.

Intolerance Scores

• loftool: 0.767
• rvis_EVS: 1.93
• rvis_percentile_EVS: 97.47

Haploinsufficiency Scores

• pHI: 0.0809
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00100

Gene Damage Prediction

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

Gene ontology

• Biological process: positive regulation of cytokine production;immunoglobulin production;immune response;T cell costimulation;positive regulation of activated T cell proliferation;positive regulation of angiogenesis
• Cellular component: extracellular space;plasma membrane;integral component of membrane
• Molecular function: protein binding;coreceptor activity