TM6SF1

transmembrane 6 superfamily member 1

Basic information

Region (hg38): 15:83107571-83144854

Links

ENSG00000136404 ∙ NCBI:53346 ∙ OMIM:606562 ∙ HGNC:11860 ∙ Uniprot:Q9BZW5 ∙ 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 TM6SF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TM6SF1 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in TM6SF1

This is a list of pathogenic ClinVar variants found in the TM6SF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-83107702-G-A		not specified	Uncertain significance (Oct 26, 2021)
15-83112799-C-A		not specified	Uncertain significance (Oct 10, 2023)
15-83112825-C-G		not specified	Uncertain significance (Sep 22, 2022)
15-83112852-G-A		not specified	Uncertain significance (Mar 21, 2024)
15-83112864-G-A		not specified	Uncertain significance (Jan 23, 2024)
15-83112882-C-T		not specified	Uncertain significance (Feb 15, 2023)
15-83112895-T-C		not specified	Uncertain significance (Dec 12, 2023)
15-83115887-T-C		not specified	Uncertain significance (Apr 23, 2024)
15-83119586-G-A			Likely benign (Jun 01, 2022)
15-83119649-G-A		not specified	Uncertain significance (Nov 27, 2023)
15-83119675-C-T		not specified	Uncertain significance (Dec 20, 2021)
15-83121938-T-C		not specified	Uncertain significance (May 18, 2022)
15-83122840-T-C		not specified	Uncertain significance (Feb 06, 2024)
15-83122855-G-A		not specified	Uncertain significance (Aug 17, 2022)
15-83126795-C-T		not specified	Uncertain significance (Dec 14, 2022)
15-83127368-A-G		not specified	Uncertain significance (Jun 26, 2023)
15-83136496-A-G		not specified	Uncertain significance (Mar 08, 2024)
15-83136497-T-C		not specified	Uncertain significance (Nov 08, 2022)
15-83136521-C-T		not specified	Uncertain significance (Apr 20, 2023)
15-83136614-G-A		not specified	Uncertain significance (Dec 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TM6SF1	protein_coding	protein_coding	ENST00000322019	10	37448

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.02e-7	0.780	125672	0	76	125748	0.000302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.999	161	201	0.802	0.00000983	2361
Missense in Polyphen		43	56.823	0.75673		682
Synonymous	-0.247	78	75.3	1.04	0.00000376	751
Loss of Function	1.40	14	20.9	0.670	0.00000106	255

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000691	0.000691
Ashkenazi Jewish	0.00	0.00
East Asian	0.000165	0.000163
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000306	0.000299
Middle Eastern	0.000165	0.000163
South Asian	0.000459	0.000457
Other	0.000654	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as sterol isomerase. {ECO:0000303|PubMed:25566323}.
• Pathway: miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.923
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.32

Haploinsufficiency Scores

• pHI: 0.181
• hipred: N
• hipred_score: 0.275
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.394

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tm6sf1

Gene ontology

• Biological process: biological_process
• Cellular component: lysosomal membrane;integral component of membrane
• Molecular function: molecular_function;protein binding