TM2D3

TM2 domain containing 3

Basic information

Region (hg38): 15:101621444-101652391

Links

ENSG00000184277 ∙ NCBI:80213 ∙ OMIM:610014 ∙ HGNC:24128 ∙ Uniprot:Q9BRN9 ∙ 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 TM2D3 gene.

• not_specified (42 variants)
• TM2D3-related_disorder (4 variants)
• NEUROCARDIORENAL_MALFORMATION_SYNDROME (3 variants)
• See_cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TM2D3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000078474.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense		2	45	1		48
nonsense		1				1
start loss						0
frameshift		1				1
splice donor/acceptor (+/-2bp)			1			1
Total	0	4	46	1	0

Highest pathogenic variant AF is 0.000011061901

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TM2D3	protein_coding	protein_coding	ENST00000333202	6	30748

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.94e-9	0.0838	125707	0	41	125748	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.743	174	149	1.17	0.00000824	1586
Missense in Polyphen		48	51.004	0.9411		527
Synonymous	-1.68	74	57.7	1.28	0.00000329	493
Loss of Function	-0.216	12	11.2	1.07	4.75e-7	135

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000513	0.000513
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000117	0.000114
Middle Eastern	0.00	0.00
South Asian	0.000362	0.000359
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.237
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.37

Haploinsufficiency Scores

• pHI: 0.117
• hipred: N
• hipred_score: 0.292
• ghis: 0.560

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.359

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tm2d3

Gene ontology

• Cellular component: integral component of membrane