TM9SF2

transmembrane 9 superfamily member 2, the group of Transmembrane 9 superfamily members

Basic information

Region (hg38): 13:99446310-99564048

Links

ENSG00000125304 ∙ NCBI:9375 ∙ OMIM:604678 ∙ HGNC:11865 ∙ Uniprot:Q99805 ∙ 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 TM9SF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TM9SF2 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			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in TM9SF2

This is a list of pathogenic ClinVar variants found in the TM9SF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-99501619-C-G		not specified	Uncertain significance (Jun 14, 2023)
13-99501625-G-C		not specified	Uncertain significance (Feb 14, 2023)
13-99501626-T-C		not specified	Likely benign (Jan 29, 2024)
13-99501630-G-C		not specified	Uncertain significance (Apr 25, 2022)
13-99501695-C-G		not specified	Uncertain significance (Jan 02, 2024)
13-99501751-G-A		not specified	Uncertain significance (Dec 14, 2021)
13-99501754-G-C		not specified	Uncertain significance (Nov 27, 2023)
13-99501755-A-T		not specified	Uncertain significance (Nov 27, 2023)
13-99517617-G-A		not specified	Uncertain significance (Jan 29, 2024)
13-99520038-T-A		not specified	Uncertain significance (Apr 25, 2023)
13-99520106-A-G		not specified	Uncertain significance (May 05, 2023)
13-99529551-G-C		not specified	Uncertain significance (Dec 12, 2023)
13-99529567-G-A		not specified	Uncertain significance (Nov 21, 2023)
13-99539514-C-T		not specified	Uncertain significance (Nov 15, 2021)
13-99540717-G-A		not specified	Uncertain significance (Jan 23, 2023)
13-99540765-A-G		not specified	Uncertain significance (Mar 20, 2024)
13-99541603-T-G		not specified	Uncertain significance (Dec 21, 2023)
13-99541666-C-T		not specified	Uncertain significance (Aug 12, 2021)
13-99547097-C-G		not specified	Uncertain significance (Nov 09, 2023)
13-99554329-A-G		not specified	Uncertain significance (Jun 28, 2022)
13-99554368-C-T		not specified	Uncertain significance (Nov 12, 2021)
13-99559463-C-T		not specified	Uncertain significance (May 23, 2023)
13-99559471-G-A		not specified	Uncertain significance (Sep 17, 2021)
13-99562719-G-C		not specified	Uncertain significance (Feb 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TM9SF2	protein_coding	protein_coding	ENST00000376387	17	62590

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000130	125731	0	2	125733	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.27	189	365	0.518	0.0000183	4361
Missense in Polyphen		41	159.7	0.25674		1933
Synonymous	-0.248	137	133	1.03	0.00000704	1246
Loss of Function	5.70	0	37.8	0.00	0.00000184	458

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: In the intracellular compartments, may function as a channel or small molecule transporter.

Recessive Scores

• pRec: 0.0938

Intolerance Scores

• loftool: 0.243
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.24

Haploinsufficiency Scores

• pHI: 0.164
• hipred: Y
• hipred_score: 0.673
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.645

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tm9sf2

Gene ontology

• Biological process: protein localization to membrane
• Cellular component: endosome;integral component of plasma membrane;endosome membrane;membrane;extracellular exosome