TMEM140

transmembrane protein 140

Basic information

Region (hg38): 7:135148071-135166215

Links

ENSG00000146859 ∙ NCBI:55281 ∙ ∙ HGNC:21870 ∙ Uniprot:Q9NV12 ∙ 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 TMEM140 gene.

• Inborn genetic diseases (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM140 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in TMEM140

This is a list of pathogenic ClinVar variants found in the TMEM140 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-135164448-G-A		not specified	Likely benign (Jan 25, 2024)
7-135164564-C-A		not specified	Uncertain significance (Feb 05, 2024)
7-135164583-G-A		not specified	Uncertain significance (Dec 13, 2023)
7-135164611-A-G		not specified	Uncertain significance (Dec 28, 2022)
7-135164706-G-A		not specified	Uncertain significance (Jan 19, 2022)
7-135164709-T-C		not specified	Uncertain significance (Feb 23, 2023)
7-135164730-G-T		not specified	Likely benign (Dec 19, 2023)
7-135164736-C-A		not specified	Uncertain significance (May 27, 2022)
7-135164754-C-G		not specified	Uncertain significance (Feb 09, 2023)
7-135164829-G-A		not specified	Uncertain significance (Sep 14, 2021)
7-135164920-T-C		not specified	Uncertain significance (Jun 06, 2022)
7-135164962-G-A		not specified	Uncertain significance (Oct 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM140	protein_coding	protein_coding	ENST00000275767	1	18144

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0540	0.717	125729	1	18	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0734	105	107	0.980	0.00000600	1170
Missense in Polyphen		29	31.02	0.93488		390
Synonymous	0.493	48	52.5	0.913	0.00000322	426
Loss of Function	0.726	2	3.46	0.579	1.50e-7	30

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.000109	0.000109
South Asian	0.000425	0.000392
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.9

Haploinsufficiency Scores

• pHI: 0.135
• hipred: N
• hipred_score: 0.123
• ghis: 0.388

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0497

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem140

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: protein binding