TM6SF2

transmembrane 6 superfamily member 2

Basic information

Region (hg38): 19:19264364-19273391

Links

ENSG00000213996 ∙ NCBI:53345 ∙ OMIM:606563 ∙ HGNC:11861 ∙ Uniprot:Q9BZW4 ∙ 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 TM6SF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TM6SF2 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			19	1	1	21
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	19	2	1

Variants in TM6SF2

This is a list of pathogenic ClinVar variants found in the TM6SF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-19264740-C-T		not specified	Uncertain significance (Mar 15, 2024)
19-19264798-C-T		not specified	Uncertain significance (Nov 03, 2022)
19-19264845-A-G		not specified	Uncertain significance (Jun 29, 2023)
19-19266494-C-T		not specified	Uncertain significance (Jul 01, 2023)
19-19266513-C-A		not specified	Uncertain significance (Jul 06, 2021)
19-19266515-A-G		not specified	Uncertain significance (Apr 04, 2023)
19-19267685-C-A		not specified	Uncertain significance (Apr 19, 2024)
19-19267993-C-T		not specified	Uncertain significance (Sep 22, 2022)
19-19267994-G-A		not specified	Uncertain significance (Dec 22, 2023)
19-19268066-C-G		not specified	Uncertain significance (Feb 13, 2024)
19-19268674-C-A		not specified	Uncertain significance (Jun 23, 2023)
19-19269727-G-A			Likely benign (May 01, 2022)
19-19269758-C-T		not specified	Uncertain significance (Jun 13, 2023)
19-19269759-G-A			Benign (Apr 18, 2018)
19-19270249-C-T		not specified	Uncertain significance (Jun 23, 2023)
19-19270254-G-A		not specified	Uncertain significance (Oct 06, 2021)
19-19270260-C-T		not specified	Uncertain significance (Sep 27, 2021)
19-19270406-A-C		not specified	Uncertain significance (Jun 05, 2023)
19-19271049-C-T		not specified	Uncertain significance (Dec 03, 2021)
19-19271072-G-A			Likely benign (Apr 01, 2023)
19-19271131-G-C			Benign (Jul 20, 2018)
19-19273160-G-A		not specified	Uncertain significance (Jun 21, 2022)
19-19273167-C-T		not specified	Uncertain significance (Feb 07, 2023)
19-19273194-C-T		not specified	Uncertain significance (Dec 27, 2022)
19-19273211-T-C		not specified	Uncertain significance (May 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TM6SF2	protein_coding	protein_coding	ENST00000389363	10	9028

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000361	0.953	124773	0	35	124808	0.000140

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.781	186	218	0.851	0.0000127	2396
Missense in Polyphen		58	75.165	0.77164		867
Synonymous	-0.0595	95	94.3	1.01	0.00000588	763
Loss of Function	1.82	10	18.4	0.543	7.84e-7	215

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000477	0.000474
Ashkenazi Jewish	0.00	0.00
East Asian	0.000479	0.000334
Finnish	0.0000509	0.0000464
European (Non-Finnish)	0.000120	0.000115
Middle Eastern	0.000479	0.000334
South Asian	0.000138	0.000131
Other	0.000339	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulator of liver fat metabolism influencing triglyceride secretion and hepatic lipid droplet content (PubMed:24531328, PubMed:24927523). May function as sterol isomerase (PubMed:25566323). {ECO:0000269|PubMed:24531328, ECO:0000269|PubMed:24927523, ECO:0000303|PubMed:25566323}.

Intolerance Scores

• loftool: 0.788
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.43

Haploinsufficiency Scores

• pHI: 0.0575
• hipred: N
• hipred_score: 0.197
• ghis: 0.409

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.335

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tm6sf2
• Phenotype: homeostasis/metabolism phenotype; digestive/alimentary phenotype; liver/biliary system phenotype

Zebrafish Information Network

• Gene name: tm6sf2
• Affected structure: enterocyte
• Phenotype tag: abnormal
• Phenotype quality: increased amount

Gene ontology

• Biological process: lipid metabolic process;regulation of lipid metabolic process
• Cellular component: endoplasmic reticulum membrane;integral component of membrane;endoplasmic reticulum-Golgi intermediate compartment membrane
• Molecular function: molecular_function;protein binding