TM4SF4

transmembrane 4 L six family member 4

Basic information

Region (hg38): 3:149474696-149503394

Links

ENSG00000169903 ∙ NCBI:7104 ∙ OMIM:606567 ∙ HGNC:11856 ∙ Uniprot:P48230 ∙ 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 TM4SF4 gene.

• Inborn genetic diseases (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TM4SF4 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			8	2		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	8	2	0

Variants in TM4SF4

This is a list of pathogenic ClinVar variants found in the TM4SF4 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-149474911-G-A		not specified	Uncertain significance (Dec 15, 2023)
3-149474924-C-T		not specified	Uncertain significance (Oct 02, 2023)
3-149474948-C-A		not specified	Uncertain significance (Oct 03, 2022)
3-149475009-A-T		not specified	Uncertain significance (Dec 09, 2023)
3-149475874-G-A		not specified	Uncertain significance (Jan 23, 2023)
3-149475890-A-T		not specified	Uncertain significance (Aug 13, 2021)
3-149475892-G-C		not specified	Uncertain significance (Mar 20, 2023)
3-149487634-A-G		not specified	Uncertain significance (Jul 21, 2021)
3-149487715-C-T		not specified	Uncertain significance (Feb 28, 2024)
3-149487751-G-T		not specified	Uncertain significance (Aug 30, 2021)
3-149498762-G-A		not specified	Likely benign (Jun 05, 2023)
3-149498772-A-G		not specified	Uncertain significance (Nov 07, 2023)
3-149498816-G-A		not specified	Likely benign (Sep 16, 2021)
3-149498816-G-T		not specified	Uncertain significance (Oct 03, 2022)
3-149498876-C-T		not specified	Uncertain significance (Dec 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TM4SF4	protein_coding	protein_coding	ENST00000305354	5	29308

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.25e-8	0.155	124569	0	82	124651	0.000329

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.181	123	117	1.05	0.00000619	1307
Missense in Polyphen		37	39.931	0.9266		459
Synonymous	-1.11	58	48.2	1.20	0.00000298	397
Loss of Function	0.0229	11	11.1	0.993	6.40e-7	113

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00119	0.00119
Ashkenazi Jewish	0.00	0.00
East Asian	0.000168	0.000167
Finnish	0.00	0.00
European (Non-Finnish)	0.000306	0.000301
Middle Eastern	0.000168	0.000167
South Asian	0.000198	0.000196
Other	0.000887	0.000826

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates the adhesive and proliferative status of intestinal epithelial cells. Can mediate density-dependent cell proliferation.

Recessive Scores

• pRec: 0.0833

Intolerance Scores

• loftool: 0.754
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.32

Haploinsufficiency Scores

• pHI: 0.212
• hipred: N
• hipred_score: 0.216
• ghis: 0.471

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0220

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tm4sf4
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: tm4sf4
• Affected structure: pancreatic A cell
• Phenotype tag: abnormal
• Phenotype quality: increased amount

Gene ontology

• Biological process: tissue regeneration
• Cellular component: integral component of membrane
• Molecular function: protein binding