TM4SF18

transmembrane 4 L six family member 18

Basic information

Region (hg38): 3:149318498-149334414

Links

ENSG00000163762 ∙ NCBI:116441 ∙ ∙ HGNC:25181 ∙ Uniprot:Q96CE8 ∙ 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 TM4SF18 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TM4SF18 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in TM4SF18

This is a list of pathogenic ClinVar variants found in the TM4SF18 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-149322269-G-A		not specified	Uncertain significance (Jan 27, 2022)
3-149322311-C-A		not specified	Uncertain significance (Feb 11, 2022)
3-149322350-A-G		not specified	Uncertain significance (May 31, 2023)
3-149322362-A-G		not specified	Uncertain significance (Apr 20, 2023)
3-149322428-G-A		not specified	Uncertain significance (Aug 10, 2021)
3-149324887-C-T		not specified	Uncertain significance (May 23, 2023)
3-149324919-A-G		not specified	Uncertain significance (Oct 18, 2021)
3-149330347-A-C		not specified	Uncertain significance (Aug 22, 2023)
3-149330398-G-T		not specified	Uncertain significance (Oct 22, 2021)
3-149330400-A-G		not specified	Uncertain significance (Apr 15, 2024)
3-149333244-C-T		not specified	Uncertain significance (Jan 23, 2023)
3-149333247-A-G		not specified	Uncertain significance (Jul 12, 2023)
3-149333291-G-A		not specified	Uncertain significance (Mar 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TM4SF18	protein_coding	protein_coding	ENST00000296059	5	15917

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000211	0.285	125632	0	113	125745	0.000449

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.127	112	108	1.03	0.00000554	1300
Missense in Polyphen		42	40.797	1.0295		498
Synonymous	0.191	39	40.5	0.962	0.00000213	391
Loss of Function	0.196	9	9.66	0.932	4.08e-7	121

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000416	0.000416
Ashkenazi Jewish	0.00	0.00
East Asian	0.00321	0.00321
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.00321	0.00321
South Asian	0.000883	0.000882
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.930
• rvis_EVS: -0.18
• rvis_percentile_EVS: 39.95

Haploinsufficiency Scores

• pHI: 0.140
• hipred: N
• hipred_score: 0.147
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.513

Gene Damage Prediction

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

Gene ontology

• Cellular component: integral component of membrane