TNMD

tenomodulin, the group of BRICHOS domain containing

Basic information

Region (hg38): X:100584936-100599885

Links

ENSG00000000005 ∙ NCBI:64102 ∙ OMIM:300459 ∙ HGNC:17757 ∙ Uniprot:Q9H2S6 ∙ 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 TNMD gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNMD 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				3	2	5
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	3	2

Variants in TNMD

This is a list of pathogenic ClinVar variants found in the TNMD 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-100585042-T-C			Benign (Jul 13, 2018)
X-100585294-A-G		not specified	Conflicting classifications of pathogenicity (Nov 03, 2021)
X-100585306-A-G		not specified	Uncertain significance (Sep 06, 2022)
X-100585333-A-G		not specified	Uncertain significance (Feb 13, 2024)
X-100593899-A-G		not specified	Uncertain significance (Jul 06, 2021)
X-100594012-T-C			Likely benign (May 01, 2022)
X-100594282-G-A		not specified	Uncertain significance (Nov 13, 2023)
X-100594284-G-C			Likely benign (Oct 01, 2022)
X-100594317-T-G		not specified	Uncertain significance (May 29, 2024)
X-100597577-G-A		not specified	Uncertain significance (Feb 17, 2024)
X-100599027-C-G		not specified	Uncertain significance (Feb 22, 2023)
X-100599086-T-G		not specified	Uncertain significance (Jul 11, 2023)
X-100599152-A-C			Benign (Jun 06, 2018)
X-100599516-T-C			Likely benign (Jun 22, 2018)
X-100599622-T-C		not specified	Uncertain significance (May 03, 2023)
X-100599646-G-A		not specified	Uncertain significance (Apr 01, 2024)
X-100599665-G-A		not specified	Uncertain significance (Jan 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNMD	protein_coding	protein_coding	ENST00000373031	7	15084

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00351	0.957	125726	4	7	125737	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.859	93	119	0.779	0.00000930	2099
Missense in Polyphen		31	49.343	0.62826		758
Synonymous	-0.464	42	38.3	1.10	0.00000299	551
Loss of Function	1.80	6	13.0	0.461	0.00000109	221

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000113	0.0000984
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000751	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000737	0.0000527
Middle Eastern	0.0000751	0.0000544
South Asian	0.000107	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be an angiogenesis inhibitor.

Recessive Scores

• pRec: 0.210

Intolerance Scores

• loftool: 0.425
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

• pHI: 0.510
• hipred: Y
• hipred_score: 0.658
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0910

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnmd
• Phenotype: skeleton phenotype; muscle phenotype

Gene ontology

• Biological process: endothelial cell morphogenesis;negative regulation of endothelial cell proliferation;negative regulation of angiogenesis;negative regulation of vascular endothelial growth factor receptor signaling pathway;tendon cell differentiation;cellular response to BMP stimulus
• Cellular component: nuclear envelope;cytoplasm;integral component of membrane
• Molecular function: protein binding