TM9SF3

transmembrane 9 superfamily member 3, the group of Transmembrane 9 superfamily members

Basic information

Region (hg38): 10:96518110-96587452

Links

ENSG00000077147 ∙ NCBI:56889 ∙ OMIM:616872 ∙ HGNC:21529 ∙ Uniprot:Q9HD45 ∙ 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 TM9SF3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TM9SF3 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	15	0	1

Variants in TM9SF3

This is a list of pathogenic ClinVar variants found in the TM9SF3 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-96522294-C-T		not specified	Uncertain significance (Oct 06, 2022)
10-96527219-T-A		not specified	Uncertain significance (Jan 31, 2022)
10-96527237-T-C		not specified	Uncertain significance (Jan 16, 2024)
10-96527429-A-G		not specified	Uncertain significance (Oct 05, 2023)
10-96527465-T-C		not specified	Uncertain significance (Feb 05, 2024)
10-96533118-G-T		not specified	Uncertain significance (May 26, 2022)
10-96544077-A-G		not specified	Uncertain significance (Mar 11, 2024)
10-96544128-T-C		not specified	Uncertain significance (Sep 22, 2023)
10-96551285-T-C		not specified	Uncertain significance (Mar 20, 2023)
10-96551294-C-CAGCAAATATCTGACATCCAGAACA			Uncertain significance (Jul 15, 2021)
10-96559738-TA-T			Benign (Jan 17, 2024)
10-96559746-A-AT			Benign (Jan 17, 2024)
10-96562090-G-A		not specified	Uncertain significance (Feb 22, 2023)
10-96562099-T-C		not specified	Uncertain significance (Mar 28, 2024)
10-96565380-T-G		not specified	Uncertain significance (Mar 21, 2023)
10-96586763-G-C		not specified	Uncertain significance (Sep 17, 2021)
10-96586768-A-G		not specified	Uncertain significance (Feb 26, 2024)
10-96586795-G-A		not specified	Uncertain significance (Jan 26, 2022)
10-96586817-C-A		not specified	Uncertain significance (Nov 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TM9SF3	protein_coding	protein_coding	ENST00000371142	15	69344

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000793	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.51	124	293	0.423	0.0000145	3835
Missense in Polyphen		25	105.57	0.23682		1322
Synonymous	0.348	90	94.3	0.954	0.00000467	1074
Loss of Function	5.32	0	33.0	0.00	0.00000169	434

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.0741
• rvis_EVS: -0.41
• rvis_percentile_EVS: 26.23

Haploinsufficiency Scores

• pHI: 0.464
• hipred: Y
• hipred_score: 0.707
• ghis: 0.690

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.268

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tm9sf3

Gene ontology

• Biological process: protein localization to membrane
• Cellular component: membrane;integral component of membrane