TM9SF1

transmembrane 9 superfamily member 1, the group of Transmembrane 9 superfamily members

Basic information

Region (hg38): 14:24189149-24195687

Links

ENSG00000100926 ∙ NCBI:10548 ∙ OMIM:618965 ∙ HGNC:11864 ∙ Uniprot:O15321 ∙ 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 TM9SF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TM9SF1 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			35			35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	0	0

Variants in TM9SF1

This is a list of pathogenic ClinVar variants found in the TM9SF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-24189443-T-C		not specified	Uncertain significance (Feb 23, 2023)
14-24189449-A-G		not specified	Uncertain significance (Dec 27, 2023)
14-24189492-G-A		not specified	Uncertain significance (Nov 07, 2022)
14-24189623-C-T		not specified	Uncertain significance (Dec 19, 2022)
14-24189635-C-T		not specified	Uncertain significance (Jun 17, 2024)
14-24189654-C-T		not specified	Uncertain significance (Dec 06, 2021)
14-24189732-A-G		not specified	Uncertain significance (Feb 15, 2023)
14-24190408-T-C		not specified	Uncertain significance (Nov 17, 2022)
14-24190448-C-A		not specified	Uncertain significance (Sep 01, 2021)
14-24190453-G-A		not specified	Uncertain significance (Jul 26, 2022)
14-24190456-C-T		not specified	Uncertain significance (Nov 10, 2022)
14-24190515-C-T		not specified	Uncertain significance (May 08, 2023)
14-24190521-A-G		not specified	Uncertain significance (Dec 28, 2023)
14-24190542-A-G		not specified	Uncertain significance (Mar 19, 2024)
14-24190605-T-C		not specified	Uncertain significance (Sep 20, 2023)
14-24190605-T-G		not specified	Uncertain significance (Dec 26, 2023)
14-24190609-C-T		not specified	Uncertain significance (Nov 18, 2022)
14-24192192-G-T		not specified	Uncertain significance (May 08, 2024)
14-24192195-T-C		not specified	Uncertain significance (Apr 13, 2023)
14-24192216-C-T		not specified	Uncertain significance (Apr 12, 2024)
14-24192230-C-T		not specified	Uncertain significance (Apr 11, 2023)
14-24192317-T-C		not specified	Uncertain significance (Jan 26, 2022)
14-24192336-G-C		not specified	Uncertain significance (Nov 06, 2023)
14-24192345-T-C		not specified	Uncertain significance (Sep 28, 2022)
14-24192657-G-A		not specified	Uncertain significance (Nov 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TM9SF1	protein_coding	protein_coding	ENST00000261789	5	24331

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.48e-7	0.957	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.11	255	369	0.691	0.0000225	3934
Missense in Polyphen		57	123.99	0.45971		1362
Synonymous	-0.100	144	142	1.01	0.00000801	1275
Loss of Function	1.96	15	25.8	0.582	0.00000159	242

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000555	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.0000555	0.0000544
South Asian	0.0000980	0.0000980
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an essential role in autophagy. {ECO:0000269|PubMed:19029833}.

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.651
• rvis_EVS: 0.18
• rvis_percentile_EVS: 66.07

Haploinsufficiency Scores

• pHI: 0.424
• hipred: N
• hipred_score: 0.274
• ghis: 0.421

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.995

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tm9sf1

Gene ontology

• Biological process: autophagy;protein localization to membrane
• Cellular component: autophagosome membrane;lysosomal membrane;membrane;integral component of membrane;cytoplasmic vesicle