TM4SF1

transmembrane 4 L six family member 1

Basic information

Region (hg38): 3:149369022-149377692

Previous symbols: [ "M3S1" ]

Links

ENSG00000169908 ∙ NCBI:4071 ∙ OMIM:191155 ∙ HGNC:11853 ∙ Uniprot:P30408 ∙ 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 TM4SF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TM4SF1 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in TM4SF1

This is a list of pathogenic ClinVar variants found in the TM4SF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-149371827-G-T		not specified	Uncertain significance (May 09, 2022)
3-149371833-T-G		not specified	Uncertain significance (Jun 23, 2021)
3-149371845-A-G		not specified	Uncertain significance (Dec 16, 2022)
3-149371854-T-C		not specified	Uncertain significance (Jan 23, 2023)
3-149375485-G-A		not specified	Uncertain significance (Nov 18, 2022)
3-149375487-A-C		not specified	Uncertain significance (Nov 18, 2022)
3-149375548-C-T		not specified	Uncertain significance (Nov 07, 2022)
3-149375564-G-A		not specified	Uncertain significance (Dec 13, 2023)
3-149375712-A-G		not specified	Uncertain significance (Mar 07, 2024)
3-149375744-A-G		not specified	Uncertain significance (Apr 30, 2024)
3-149377414-C-A		not specified	Uncertain significance (May 20, 2024)
3-149377525-C-T		not specified	Uncertain significance (Apr 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TM4SF1	protein_coding	protein_coding	ENST00000305366	5	8844

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00156	0.892	125714	0	34	125748	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0137	115	115	1.00	0.00000600	1304
Missense in Polyphen		39	44.826	0.87003		531
Synonymous	0.131	45	46.1	0.975	0.00000262	412
Loss of Function	1.40	6	11.0	0.544	6.68e-7	114

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000325	0.000325
Ashkenazi Jewish	0.00	0.00
East Asian	0.000435	0.000435
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000969	0.0000967
Middle Eastern	0.000435	0.000435
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.669
• rvis_EVS: -0.3
• rvis_percentile_EVS: 32.62

Haploinsufficiency Scores

• pHI: 0.193
• hipred: Y
• hipred_score: 0.692
• ghis: 0.490

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.987

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tm4sf1

Gene ontology

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