TEDDM1

transmembrane epididymal protein 1

Basic information

Region (hg38): 1:182398117-182400667

Links

ENSG00000203730 ∙ NCBI:127670 ∙ OMIM:620288 ∙ HGNC:30233 ∙ Uniprot:Q5T9Z0 ∙ 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 TEDDM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TEDDM1 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			16	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	0

Variants in TEDDM1

This is a list of pathogenic ClinVar variants found in the TEDDM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-182399684-G-T		not specified	Uncertain significance (Mar 28, 2023)
1-182399716-T-A		not specified	Uncertain significance (Dec 04, 2023)
1-182399761-T-C		not specified	Uncertain significance (May 09, 2022)
1-182399765-A-G		not specified	Uncertain significance (Jun 10, 2022)
1-182399803-C-A		not specified	Uncertain significance (Nov 10, 2021)
1-182399819-A-G		not specified	Uncertain significance (Jun 28, 2022)
1-182399879-A-G		not specified	Uncertain significance (Nov 19, 2022)
1-182399898-C-G		not specified	Uncertain significance (Jun 28, 2022)
1-182399904-G-T		not specified	Uncertain significance (Dec 22, 2023)
1-182399963-C-G		not specified	Uncertain significance (Dec 12, 2023)
1-182400030-G-T		not specified	Uncertain significance (Nov 17, 2022)
1-182400043-A-C		not specified	Uncertain significance (Aug 12, 2022)
1-182400077-C-A		not specified	Uncertain significance (Jan 23, 2023)
1-182400077-C-T		not specified	Uncertain significance (Nov 06, 2023)
1-182400173-C-A		not specified	Uncertain significance (May 30, 2024)
1-182400226-A-T		not specified	Uncertain significance (Oct 05, 2021)
1-182400325-A-G		not specified	Uncertain significance (Jul 06, 2021)
1-182400353-C-T		not specified	Likely benign (Oct 10, 2023)
1-182400424-G-C		not specified	Uncertain significance (Jun 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TEDDM1	protein_coding	protein_coding	ENST00000367565	1	2500

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00220	0.537	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.365	148	136	1.09	0.00000631	1768
Missense in Polyphen		31	36.481	0.84975		513
Synonymous	-0.586	63	57.4	1.10	0.00000295	553
Loss of Function	0.214	4	4.49	0.891	1.92e-7	64

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.666
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.23

Haploinsufficiency Scores

• pHI: 0.187
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0263

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Teddm1b

Gene ontology

• Cellular component: integral component of membrane