TM7SF3

transmembrane 7 superfamily member 3

Basic information

Region (hg38): 12:26971579-27014434

Links

ENSG00000064115 ∙ NCBI:51768 ∙ OMIM:605181 ∙ HGNC:23049 ∙ Uniprot:Q9NS93 ∙ 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 TM7SF3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TM7SF3 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			18		1	19
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	0	1

Variants in TM7SF3

This is a list of pathogenic ClinVar variants found in the TM7SF3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-26974015-G-A		not specified	Uncertain significance (Apr 27, 2024)
12-26974018-C-T		not specified	Uncertain significance (Aug 18, 2021)
12-26974066-T-C		not specified	Uncertain significance (Feb 14, 2023)
12-26974102-G-A		not specified	Uncertain significance (Apr 07, 2023)
12-26974152-C-T		not specified	Likely benign (Apr 12, 2024)
12-26974200-A-G		not specified	Uncertain significance (Apr 09, 2024)
12-26976304-T-C		not specified	Uncertain significance (Apr 20, 2024)
12-26979792-G-T		not specified	Uncertain significance (Jan 26, 2023)
12-26979796-A-G		not specified	Uncertain significance (Dec 27, 2022)
12-26982791-G-A		not specified	Uncertain significance (Aug 14, 2023)
12-26990501-G-C		not specified	Uncertain significance (Oct 05, 2021)
12-26990537-G-T		not specified	Uncertain significance (Apr 08, 2023)
12-26990554-T-C		not specified	Uncertain significance (Mar 14, 2023)
12-26990618-G-C		not specified	Uncertain significance (May 01, 2024)
12-26995299-T-G		not specified	Uncertain significance (May 15, 2024)
12-26995364-G-C		not specified	Uncertain significance (Oct 06, 2023)
12-26995391-G-C			Benign (Feb 19, 2018)
12-26996745-G-A		not specified	Uncertain significance (May 04, 2023)
12-26996781-G-A		not specified	Uncertain significance (Dec 21, 2023)
12-26999550-T-C		not specified	Uncertain significance (Jul 08, 2022)
12-26999585-C-A		not specified	Uncertain significance (Apr 03, 2023)
12-26999597-G-A		not specified	Uncertain significance (May 29, 2024)
12-26999601-A-C		not specified	Uncertain significance (Oct 20, 2021)
12-26999673-G-A		not specified	Uncertain significance (Jul 16, 2021)
12-26999673-G-C		not specified	Uncertain significance (May 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TM7SF3	protein_coding	protein_coding	ENST00000343028	12	41240

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.56e-8	0.983	125664	0	83	125747	0.000330

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.893	262	306	0.856	0.0000153	3702
Missense in Polyphen		69	97.394	0.70846		1263
Synonymous	0.177	119	121	0.980	0.00000692	1138
Loss of Function	2.23	16	28.9	0.553	0.00000156	321

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00126	0.00126
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000265	0.000211
Middle Eastern	0.000381	0.000381
South Asian	0.000490	0.000490
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the inhibition of cytokine-induced death of pancreatic beta cells. Involved in the promotion of insulin secretion from pancreatic beta cells (PubMed:21853325). Is a downstream transcriptional target of p53/TP53, and acts as a pro- survival homeostatic factor that attenuates the development of cellular stress. Maintains protein homeostasis and promotes cell survival through attenuation of endoplasmic reticulum (ER) stress and the subsequent induction of unfolded protein response (UPR) (PubMed:27740623). {ECO:0000269|PubMed:21853325, ECO:0000269|PubMed:27740623}.

Recessive Scores

• pRec: 0.0953

Intolerance Scores

• loftool: 0.791
• rvis_EVS: -0.16
• rvis_percentile_EVS: 42.06

Haploinsufficiency Scores

• pHI: 0.128
• hipred: N
• hipred_score: 0.492
• ghis: 0.508

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.517

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tm7sf3

Gene ontology

• Biological process: positive regulation of insulin secretion;cellular response to unfolded protein;negative regulation of programmed cell death
• Cellular component: plasma membrane;integral component of membrane;extracellular exosome
• Molecular function: molecular_function