TMEM198

transmembrane protein 198

Basic information

Region (hg38): 2:219543663-219550595

Links

ENSG00000188760 ∙ NCBI:130612 ∙ ∙ HGNC:33704 ∙ Uniprot:Q66K66 ∙ 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 TMEM198 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM198 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in TMEM198

This is a list of pathogenic ClinVar variants found in the TMEM198 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-219544797-G-A		not specified	Uncertain significance (Dec 18, 2023)
2-219544810-A-G		not specified	Uncertain significance (Nov 21, 2022)
2-219544822-G-A		not specified	Uncertain significance (May 26, 2023)
2-219547557-C-T		not specified	Uncertain significance (Mar 08, 2024)
2-219547574-C-T		not specified	Uncertain significance (Apr 27, 2022)
2-219547752-C-T		not specified	Uncertain significance (Mar 22, 2023)
2-219547805-G-A		not specified	Uncertain significance (Apr 05, 2023)
2-219547835-C-T		not specified	Uncertain significance (Jun 24, 2022)
2-219547836-G-A		not specified	Uncertain significance (Mar 01, 2023)
2-219547871-G-A		not specified	Uncertain significance (Jan 19, 2024)
2-219547901-G-A		not specified	Uncertain significance (Sep 28, 2022)
2-219547913-G-T		not specified	Uncertain significance (May 06, 2022)
2-219547914-C-T		not specified	Uncertain significance (Jul 25, 2023)
2-219547934-C-A		not specified	Uncertain significance (Apr 24, 2024)
2-219547947-A-G		not specified	Uncertain significance (Jul 17, 2023)
2-219548039-G-T		not specified	Uncertain significance (Apr 18, 2023)
2-219548076-C-T		not specified	Uncertain significance (Aug 21, 2023)
2-219549176-G-A		not specified	Uncertain significance (Apr 25, 2022)
2-219549190-C-T		not specified	Uncertain significance (Jul 14, 2021)
2-219549292-G-T		not specified	Uncertain significance (Oct 26, 2022)
2-219549329-G-A		not specified	Uncertain significance (Sep 27, 2021)
2-219549334-A-G		not specified	Uncertain significance (Jan 31, 2024)
2-219549841-C-T		not specified	Uncertain significance (May 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM198	protein_coding	protein_coding	ENST00000344458	4	6933

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.407	0.592	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	190	235	0.810	0.0000165	2199
Missense in Polyphen		16	29.272	0.5466		320
Synonymous	-0.449	109	103	1.06	0.00000650	872
Loss of Function	2.69	3	13.8	0.218	9.11e-7	122

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000108	0.000105
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes LRP6 phosphorylation by casein kinases and thereby plays a role in Wnt signaling. May be a membrane scaffold protein involved in the self-aggregation of LRP6 to further enhance its activity. {ECO:0000269|PubMed:21536646}.

Intolerance Scores

• loftool: 0.404
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.51

Haploinsufficiency Scores

• pHI: 0.315
• hipred: N
• hipred_score: 0.402
• ghis: 0.613

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.480

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem198

Gene ontology

• Biological process: multicellular organism development;Wnt signaling pathway;positive regulation of canonical Wnt signaling pathway
• Cellular component: plasma membrane;integral component of membrane;cytoplasmic vesicle