TENM1

teneurin transmembrane protein 1, the group of Teneurin transmembrane protein family

Basic information

Region (hg38): X:124375903-125204312

Previous symbols: [ "ODZ3", "TNM", "ODZ1" ]

Links

ENSG00000009694 ∙ NCBI:10178 ∙ OMIM:300588 ∙ HGNC:8117 ∙ Uniprot:Q9UKZ4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• isolated congenital anosmia (Supportive), mode of inheritance: AD
• cerebral palsy (Limited), mode of inheritance: XL
• anosmia (Limited), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Microphthalmia, isolated, with coloboma 9	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	22766609

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TENM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TENM1 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				15	16	31
missense			76	13	3	92
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	3	5
non coding					16	16
Total	0	0	77	28	35

Variants in TENM1

This is a list of pathogenic ClinVar variants found in the TENM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-124380579-T-C		TENM1-related disorder	Likely benign (Apr 24, 2019)
X-124380599-T-G		not specified	Uncertain significance (Mar 30, 2024)
X-124380710-C-A			Uncertain significance (Apr 01, 2022)
X-124380732-T-G		not specified	Uncertain significance (Feb 05, 2024)
X-124380755-G-A		TENM1-related disorder	Benign (Oct 09, 2018)
X-124381030-T-C		not specified	Uncertain significance (Jan 16, 2024)
X-124381068-C-T		not specified	Uncertain significance (May 08, 2024)
X-124381148-A-C		not specified	Uncertain significance (May 14, 2024)
X-124381186-C-T		TENM1-related disorder	Likely benign (Apr 24, 2019)
X-124381201-G-A		not specified	Uncertain significance (Sep 19, 2023)
X-124382691-A-C		TENM1-related disorder	Likely benign (Apr 24, 2019)
X-124382708-G-A		not specified	Uncertain significance (Jul 05, 2023)
X-124382768-C-T		not specified	Uncertain significance (Feb 02, 2024)
X-124383680-A-C		not specified	Uncertain significance (May 09, 2023)
X-124383921-C-T		not specified	Uncertain significance (Jul 14, 2022)
X-124384061-C-T		TENM1-related disorder	Benign (Jan 28, 2020)
X-124384138-C-T		not specified	Uncertain significance (Oct 25, 2023)
X-124384176-G-C			Benign (Dec 31, 2019)
X-124384208-C-T			Benign (Dec 11, 2017)
X-124384350-T-C		not specified	Uncertain significance (Dec 07, 2021)
X-124384356-T-A		TENM1-related disorder	Likely benign (Dec 31, 2019)
X-124384361-T-A		not specified	Uncertain significance (Nov 30, 2022)
X-124384398-C-T		not specified	Uncertain significance (May 30, 2024)
X-124384399-G-A		not specified	Uncertain significance (Mar 08, 2024)
X-124384506-A-G		not specified	Uncertain significance (Apr 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TENM1	protein_coding	protein_coding	ENST00000422452	32	587914

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.29e-7	125733	4	6	125743	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.43	748	1.06e+3	0.704	0.0000818	17972
Missense in Polyphen		144	295.8	0.48681		4711
Synonymous	0.358	394	403	0.977	0.0000319	5329
Loss of Function	7.71	10	88.1	0.114	0.00000701	1445

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000731	0.0000731
Ashkenazi Jewish	0.000134	0.0000992
East Asian	0.0000729	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000737	0.0000527
Middle Eastern	0.0000729	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in neural development, regulating the establishment of proper connectivity within the nervous system. May function as a cellular signal transducer (By similarity). {ECO:0000250}.; FUNCTION: Ten-1 intracellular domain: Induces gene transcription activation. {ECO:0000250}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• rvis_EVS: -3.46
• rvis_percentile_EVS: 0.36

Haploinsufficiency Scores

• pHI: 0.487
• hipred: Y
• hipred_score: 0.685
• ghis: 0.595

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tenm1

Gene ontology

• Biological process: regulation of transcription by RNA polymerase III;immune response;heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules;neuropeptide signaling pathway;nervous system development;negative regulation of cell population proliferation;positive regulation of actin filament polymerization;positive regulation of peptidyl-serine phosphorylation;positive regulation of MAP kinase activity;neuron development;positive regulation of filopodium assembly;positive regulation of intracellular protein transport
• Cellular component: extracellular region;nucleus;cytoplasm;endoplasmic reticulum;Golgi apparatus;cytoskeleton;plasma membrane;integral component of plasma membrane;nuclear matrix;nuclear speck;neuron projection;perinuclear region of cytoplasm
• Molecular function: heparin binding;protein homodimerization activity;protein heterodimerization activity;cell adhesion molecule binding