TMEM120B

transmembrane protein 120B

Basic information

Region (hg38): 12:121712752-121783001

Links

ENSG00000188735 ∙ NCBI:144404 ∙ OMIM:616551 ∙ HGNC:32008 ∙ Uniprot:A0PK00 ∙ 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 TMEM120B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM120B 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				1		1
missense			20	1		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			7	1		8
Total	0	0	27	3	0

Variants in TMEM120B

This is a list of pathogenic ClinVar variants found in the TMEM120B region.

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

Position	Type	Phenotype	Significance	ClinVar
12-121712930-G-C		not specified	Uncertain significance (Jul 27, 2022)
12-121712932-C-G		not specified	Uncertain significance (Nov 09, 2023)
12-121743638-A-G		not specified	Uncertain significance (Mar 01, 2023)
12-121743648-A-G		not specified	Likely benign (Jan 08, 2024)
12-121743672-C-T		not specified	Uncertain significance (Nov 26, 2024)
12-121743680-A-G		not specified	Uncertain significance (Oct 08, 2024)
12-121743681-C-T		not specified	Uncertain significance (Feb 22, 2023)
12-121743696-C-G		not specified	Uncertain significance (Sep 25, 2024)
12-121743734-C-T		not specified	Uncertain significance (Nov 29, 2021)
12-121748329-C-G		not specified	Uncertain significance (Oct 17, 2023)
12-121748333-C-G		not specified	Uncertain significance (Sep 20, 2023)
12-121748367-A-G		not specified	Uncertain significance (Jul 09, 2024)
12-121748379-C-G		not specified	Uncertain significance (Dec 20, 2021)
12-121748420-G-A		not specified	Uncertain significance (Dec 15, 2023)
12-121748420-G-T		not specified	Uncertain significance (Oct 04, 2022)
12-121748441-G-A		not specified	Uncertain significance (Nov 09, 2024)
12-121750397-T-G		not specified	Uncertain significance (Dec 03, 2024)
12-121750435-G-A		not specified	Uncertain significance (Apr 01, 2024)
12-121752168-C-T			Likely benign (Mar 01, 2024)
12-121761658-C-A		not specified	Uncertain significance (Dec 17, 2023)
12-121761698-C-G		not specified	Uncertain significance (Apr 12, 2023)
12-121761722-A-C		not specified	Uncertain significance (Dec 12, 2023)
12-121770960-T-C		Exstrophy-epispadias complex	Uncertain significance (-)
12-121771532-C-G		not specified	Uncertain significance (Aug 28, 2024)
12-121773421-G-A		not specified	Uncertain significance (Aug 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM120B	protein_coding	protein_coding	ENST00000449592	12	70250

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00712	0.992	124781	0	28	124809	0.000112

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.966	156	194	0.805	0.0000112	2212
Missense in Polyphen		36	68.261	0.52738		797
Synonymous	-0.494	92	86.2	1.07	0.00000572	616
Loss of Function	2.98	8	23.6	0.339	0.00000108	261

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000475	0.000475
Ashkenazi Jewish	0.00	0.00
East Asian	0.000205	0.000167
Finnish	0.00	0.00
European (Non-Finnish)	0.000116	0.000115
Middle Eastern	0.000205	0.000167
South Asian	0.0000985	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Necessary for efficient adipogenesis. {ECO:0000250|UniProtKB:Q3TA38}.

Recessive Scores

• pRec: 0.0903

Intolerance Scores

• loftool: 0.488
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.26

Haploinsufficiency Scores

• pHI: 0.220
• hipred: Y
• hipred_score: 0.641
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.131

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem120b

Gene ontology

• Biological process: biological_process;fat cell differentiation;protein heterooligomerization
• Cellular component: cellular_component;nuclear inner membrane;integral component of membrane
• Molecular function: molecular_function;protein binding