NTM

neurotrimin, the group of I-set domain containing|IgLON cell adhesion molecules

Basic information

Region (hg38): 11:131370477-132336822

Links

ENSG00000182667 ∙ NCBI:50863 ∙ OMIM:607938 ∙ HGNC:17941 ∙ Uniprot:Q9P121 ∙ 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 NTM gene.

• Inborn genetic diseases (7 variants)
• Connective tissue disorder (3 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NTM 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					2	2
missense			6	3		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	6	3	2

Variants in NTM

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

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

Position	Type	Phenotype	Significance	ClinVar
11-131911534-C-G		not specified	Uncertain significance (Dec 26, 2023)
11-131911576-G-T		not specified	Uncertain significance (Dec 12, 2023)
11-131911606-T-C		not specified	Uncertain significance (Oct 17, 2023)
11-131911625-G-T			Benign (Apr 10, 2018)
11-131911634-G-C		not specified	Uncertain significance (Feb 17, 2024)
11-132146289-A-G		not specified	Uncertain significance (Apr 19, 2023)
11-132146402-G-A			Benign (Apr 10, 2018)
11-132146404-A-C		not specified	Uncertain significance (Mar 27, 2023)
11-132212039-G-A		not specified	Uncertain significance (Feb 06, 2024)
11-132307685-G-A		Connective tissue disorder	Likely benign (Jun 01, 2018)
11-132307788-C-T		not specified	Uncertain significance (Apr 08, 2022)
11-132314588-C-G		not specified	Uncertain significance (May 09, 2023)
11-132314655-G-A		not specified	Uncertain significance (May 23, 2023)
11-132330155-G-A		Connective tissue disorder	Likely benign (Jun 01, 2018)
11-132335070-G-A		not specified	Likely benign (Dec 20, 2021)
11-132335082-C-T		Connective tissue disorder	Likely benign (Jun 01, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NTM	protein_coding	protein_coding	ENST00000425719	8	966344

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0578	0.939	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.20	161	210	0.768	0.0000118	2284
Missense in Polyphen		47	88.755	0.52955		952
Synonymous	-0.282	94	90.6	1.04	0.00000578	727
Loss of Function	2.57	5	16.1	0.310	6.85e-7	198

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000618	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Neural cell adhesion molecule.
• Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Intolerance Scores

• loftool: 0.505
• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.19

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.646
• ghis: 0.598

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ntm

Gene ontology

• Biological process: cell adhesion;neuron recognition
• Cellular component: extracellular region;plasma membrane;anchored component of membrane
• Molecular function: protein binding