TM2D1

TM2 domain containing 1

Basic information

Region (hg38): 1:61681046-61725423

Links

ENSG00000162604 ∙ NCBI:83941 ∙ OMIM:610080 ∙ HGNC:24142 ∙ Uniprot:Q9BX74 ∙ 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 TM2D1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TM2D1 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			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in TM2D1

This is a list of pathogenic ClinVar variants found in the TM2D1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-61683497-G-A		not specified	Uncertain significance (Aug 02, 2023)
1-61683516-T-A		not specified	Uncertain significance (Jun 29, 2022)
1-61694768-A-C		not specified	Uncertain significance (Jun 13, 2023)
1-61700997-C-T		not specified	Uncertain significance (Feb 17, 2022)
1-61709343-T-C		not specified	Uncertain significance (Mar 20, 2024)
1-61723731-T-C		not specified	Uncertain significance (Nov 05, 2021)
1-61723751-G-A		not specified	Uncertain significance (Feb 23, 2023)
1-61724967-T-C		not specified	Uncertain significance (Jun 18, 2024)
1-61724975-T-C		not specified	Uncertain significance (Sep 01, 2021)
1-61724999-C-G		not specified	Uncertain significance (Aug 12, 2022)
1-61725024-A-C		not specified	Uncertain significance (Dec 19, 2022)
1-61725045-C-G		not specified	Uncertain significance (Sep 22, 2023)
1-61725059-C-A		not specified	Uncertain significance (Apr 09, 2024)
1-61725063-C-T		not specified	Uncertain significance (Sep 27, 2022)
1-61725087-G-C		not specified	Uncertain significance (Mar 26, 2024)
1-61725092-G-A		not specified	Uncertain significance (Oct 03, 2022)
1-61725096-G-A		not specified	Uncertain significance (Aug 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TM2D1	protein_coding	protein_coding	ENST00000371180	6	44378

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000110	0.834	124608	0	10	124618	0.0000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.128	132	136	0.969	0.00000641	1701
Missense in Polyphen		31	47.807	0.64844		640
Synonymous	-0.337	59	55.8	1.06	0.00000270	554
Loss of Function	1.27	8	12.9	0.618	6.99e-7	155

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000962	0.0000961
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000536	0.0000531
Middle Eastern	0.00	0.00
South Asian	0.0000334	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May participate in amyloid-beta-induced apoptosis via its interaction with beta-APP42. {ECO:0000269|PubMed:11278849, ECO:0000269|PubMed:12836168}.

Recessive Scores

• pRec: 0.0989

Haploinsufficiency Scores

• pHI: 0.344
• hipred: N
• hipred_score: 0.235
• ghis: 0.420

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00420

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tm2d1

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;apoptotic signaling pathway
• Cellular component: nucleoplasm;integral component of plasma membrane
• Molecular function: amyloid-beta binding;G protein-coupled receptor activity