TM7SF2

transmembrane 7 superfamily member 2

Basic information

Region (hg38): 11:65111845-65116384

Links

ENSG00000149809 ∙ NCBI:7108 ∙ OMIM:603414 ∙ HGNC:11863 ∙ Uniprot:O76062 ∙ 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 TM7SF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TM7SF2 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			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	25	1	1

Variants in TM7SF2

This is a list of pathogenic ClinVar variants found in the TM7SF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-65112043-C-T		not specified	Uncertain significance (Sep 14, 2023)
11-65112055-G-C		not specified	Uncertain significance (Oct 20, 2021)
11-65112547-A-G		not specified	Uncertain significance (Jan 30, 2024)
11-65112578-C-G		not specified	Uncertain significance (Jun 18, 2021)
11-65112580-G-C		not specified	Uncertain significance (Dec 08, 2022)
11-65112618-G-G			Likely benign (Jun 20, 2017)
11-65112686-C-T		not specified	Uncertain significance (Feb 28, 2023)
11-65112706-C-G		not specified	Uncertain significance (Jan 23, 2023)
11-65112817-G-A		not specified	Uncertain significance (Jan 09, 2024)
11-65113350-C-A		not specified	Uncertain significance (Mar 22, 2022)
11-65113363-A-G		not specified	Uncertain significance (Jul 15, 2021)
11-65113370-C-G		not specified	Uncertain significance (Apr 19, 2023)
11-65113372-C-A		not specified	Uncertain significance (Jun 27, 2023)
11-65113565-T-A		not specified	Uncertain significance (Mar 15, 2024)
11-65114773-G-A		not specified	Uncertain significance (Sep 27, 2022)
11-65114777-T-C		not specified	Uncertain significance (Sep 14, 2023)
11-65114934-G-T		not specified	Uncertain significance (May 08, 2023)
11-65114949-G-A		not specified	Uncertain significance (Oct 03, 2022)
11-65114949-G-T		not specified	Uncertain significance (Sep 27, 2022)
11-65114952-T-C		not specified	Uncertain significance (Feb 10, 2022)
11-65115326-A-G		not specified	Uncertain significance (Feb 16, 2023)
11-65115340-G-T		not specified	Uncertain significance (Apr 19, 2023)
11-65115359-C-T		not specified	Uncertain significance (May 15, 2024)
11-65115365-G-A		not specified	Uncertain significance (Oct 20, 2021)
11-65115382-C-T		not specified	Uncertain significance (Mar 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TM7SF2	protein_coding	protein_coding	ENST00000279263	10	4540

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.37e-7	0.831	124759	0	51	124810	0.000204

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.404	221	239	0.926	0.0000135	2600
Missense in Polyphen		103	123.42	0.83454		1349
Synonymous	0.339	101	105	0.958	0.00000586	916
Loss of Function	1.50	14	21.5	0.651	0.00000119	214

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000439	0.000438
Ashkenazi Jewish	0.00	0.00
East Asian	0.000279	0.000278
Finnish	0.0000928	0.0000928
European (Non-Finnish)	0.000249	0.000247
Middle Eastern	0.000279	0.000278
South Asian	0.000163	0.000163
Other	0.000363	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the conversion of lanosterol to cholesterol. {ECO:0000269|PubMed:11784322}.
• Pathway: Steroid biosynthesis - Homo sapiens (human);Simvastatin Action Pathway;Pravastatin Action Pathway;Atorvastatin Action Pathway;Hyper-IgD syndrome;Cholesteryl ester storage disease;Lysosomal Acid Lipase Deficiency (Wolman Disease);Alendronate Action Pathway;Rosuvastatin Action Pathway;Lovastatin Action Pathway;Mevalonic aciduria;Wolman disease;Risedronate Action Pathway;Cerivastatin Action Pathway;Pamidronate Action Pathway;Fluvastatin Action Pathway;Smith-Lemli-Opitz Syndrome (SLOS);Chondrodysplasia Punctata II, X Linked Dominant (CDPX2);CHILD Syndrome;Desmosterolosis;Hypercholesterolemia;Steroid Biosynthesis;Zoledronate Action Pathway;Ibandronate Action Pathway;Activation of gene expression by SREBF (SREBP);Metabolism of lipids;zymosterol biosynthesis;Regulation of cholesterol biosynthesis by SREBP (SREBF);Squalene and cholesterol biosynthesis;Metabolism;cholesterol biosynthesis III (via desmosterol);cholesterol biosynthesis II (via 24,25-dihydrolanosterol);superpathway of cholesterol biosynthesis;Metabolism of steroids;cholesterol biosynthesis I;Cholesterol biosynthesis;Activation of gene expression by SREBF (SREBP) (Consensus)

Intolerance Scores

• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.88

Haploinsufficiency Scores

• pHI: 0.0980
• hipred: N
• hipred_score: 0.335
• ghis: 0.461

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.848

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tm7sf2
• Phenotype: skeleton phenotype; immune system phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; craniofacial phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: cholesterol biosynthetic process;sterol biosynthetic process;regulation of cholesterol biosynthetic process;oxidation-reduction process
• Cellular component: nuclear inner membrane;endoplasmic reticulum;endoplasmic reticulum membrane;integral component of plasma membrane;integral component of endoplasmic reticulum membrane;intracellular membrane-bounded organelle;receptor complex
• Molecular function: delta14-sterol reductase activity;NADP binding