TMIGD1

transmembrane and immunoglobulin domain containing 1, the group of I-set domain containing

Basic information

Region (hg38): 17:30316333-30334059

Previous symbols: [ "TMIGD" ]

Links

ENSG00000182271 ∙ NCBI:388364 ∙ ∙ HGNC:32431 ∙ Uniprot:Q6UXZ0 ∙ 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 TMIGD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMIGD1 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			15	4		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	4	0

Variants in TMIGD1

This is a list of pathogenic ClinVar variants found in the TMIGD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-30318899-C-A		not specified	Uncertain significance (Jun 11, 2024)
17-30324834-A-T		not specified	Uncertain significance (Dec 22, 2023)
17-30324874-A-T		not specified	Uncertain significance (Sep 13, 2023)
17-30324891-C-T		not specified	Uncertain significance (Jun 03, 2022)
17-30324915-A-G		not specified	Uncertain significance (Aug 04, 2021)
17-30324935-G-A		not specified	Uncertain significance (Sep 22, 2022)
17-30324953-C-T		not specified	Likely benign (Feb 15, 2023)
17-30324954-G-A		not specified	Uncertain significance (Jul 13, 2021)
17-30324956-C-T		not specified	Likely benign (Mar 23, 2022)
17-30325025-T-C		not specified	Likely benign (Apr 07, 2023)
17-30325028-C-A		not specified	Uncertain significance (Aug 02, 2021)
17-30325071-C-T		not specified	Likely benign (Dec 17, 2021)
17-30329292-C-T		not specified	Uncertain significance (Mar 27, 2023)
17-30329364-T-C		not specified	Uncertain significance (Dec 13, 2022)
17-30329374-T-G		not specified	Uncertain significance (Apr 14, 2022)
17-30329376-C-G		not specified	Uncertain significance (Aug 17, 2022)
17-30329397-C-G		not specified	Uncertain significance (Apr 04, 2024)
17-30329412-C-A		not specified	Uncertain significance (Oct 04, 2022)
17-30329452-A-G		not specified	Uncertain significance (Jan 09, 2024)
17-30332087-A-G		not specified	Uncertain significance (Dec 07, 2023)
17-30332087-A-T		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMIGD1	protein_coding	protein_coding	ENST00000328886	6	17727

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.13e-7	0.275	125681	0	65	125746	0.000258

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.732	164	140	1.17	0.00000714	1736
Missense in Polyphen		50	45.609	1.0963		610
Synonymous	0.478	48	52.4	0.916	0.00000302	489
Loss of Function	0.376	11	12.4	0.885	6.13e-7	152

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000825	0.000825
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000318	0.000316
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May control cell-cell adhesion, cell migration and proliferation, cell morphology, and protects renal epithelial cells from oxidative cell injury to promote cell survival. {ECO:0000269|PubMed:26342724}.

Intolerance Scores

• loftool: 0.745
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.74

Haploinsufficiency Scores

• pHI: 0.0535
• hipred: N
• hipred_score: 0.210
• ghis: 0.391

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00309

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmigd1

Gene ontology

• Biological process: regulation of cell migration;regulation of cell population proliferation;negative regulation of apoptotic process;regulation of membrane permeability
• Cellular component: cytoplasm;plasma membrane;integral component of membrane