TM2D2

TM2 domain containing 2

Basic information

Region (hg38): 8:38988808-38996824

Links

ENSG00000169490 ∙ NCBI:83877 ∙ OMIM:610081 ∙ HGNC:24127 ∙ Uniprot:Q9BX73 ∙ 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 TM2D2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TM2D2 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			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	15	1	0

Variants in TM2D2

This is a list of pathogenic ClinVar variants found in the TM2D2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-38991526-T-C		not specified	Uncertain significance (May 28, 2024)
8-38991538-C-T		not specified	Uncertain significance (Nov 17, 2022)
8-38993593-T-C		not specified	Uncertain significance (Apr 13, 2022)
8-38993600-C-T		not specified	Uncertain significance (Sep 14, 2022)
8-38993657-C-T		not specified	Uncertain significance (Jan 22, 2024)
8-38995350-C-T		not specified	Uncertain significance (Oct 03, 2023)
8-38995364-A-G		not specified	Uncertain significance (Sep 27, 2022)
8-38996226-G-A		not specified	Uncertain significance (Aug 22, 2023)
8-38996234-G-A		not specified	Uncertain significance (Dec 18, 2023)
8-38996261-C-T		not specified	Likely benign (Jul 14, 2021)
8-38996285-G-A		not specified	Uncertain significance (Feb 11, 2022)
8-38996292-C-A		not specified	Uncertain significance (Oct 25, 2022)
8-38996295-C-G		not specified	Uncertain significance (Aug 09, 2021)
8-38996306-G-A		not specified	Uncertain significance (Apr 23, 2024)
8-38996310-G-C		not specified	Uncertain significance (Apr 18, 2023)
8-38996373-T-C		not specified	Uncertain significance (Sep 13, 2023)
8-38996406-G-A		not specified	Uncertain significance (Dec 30, 2023)
8-38996417-A-G		not specified	Uncertain significance (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TM2D2	protein_coding	protein_coding	ENST00000456397	4	8017

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00645	0.920	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.480	105	120	0.877	0.00000580	1367
Missense in Polyphen		26	40.325	0.64477		458
Synonymous	0.419	48	51.8	0.926	0.00000271	450
Loss of Function	1.54	5	10.3	0.484	6.00e-7	115

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000204	0.000202
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.302
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.19

Haploinsufficiency Scores

• pHI: 0.123
• hipred: N
• hipred_score: 0.369
• ghis: 0.632

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.341

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tm2d2

Gene ontology

• Cellular component: integral component of membrane