TMPPE

transmembrane protein with metallophosphoesterase domain

Basic information

Region (hg38): 3:33090420-33097146

Links

ENSG00000188167 ∙ NCBI:643853 ∙ ∙ HGNC:33865 ∙ Uniprot:Q6ZT21 ∙ 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 TMPPE gene.

• Inborn genetic diseases (20 variants)
• Mucopolysaccharidosis, MPS-IV-B;GM1 gangliosidosis (19 variants)
• GM1 gangliosidosis;Mucopolysaccharidosis, MPS-IV-B (14 variants)
• not provided (11 variants)
• GM1 gangliosidosis (9 variants)
• Infantile GM1 gangliosidosis (8 variants)
• Mucopolysaccharidosis, MPS-IV-B (8 variants)
• not specified (4 variants)
• GM1 gangliosidosis type 3 (3 variants)
• GM1 gangliosidosis type 2 (3 variants)
• - (1 variants)
• Mucopolysaccharidosis, MPS-IV-B;GM1 gangliosidosis type 2;GM1 gangliosidosis type 3;Infantile GM1 gangliosidosis (1 variants)
• Morquio syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMPPE 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			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	4	3	13	17	3	40
Total	4	3	30	18	3

Highest pathogenic variant AF is 0.000197

Variants in TMPPE

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

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

Position	Type	Phenotype	Significance	ClinVar
3-33092913-C-T		not specified	Uncertain significance (Aug 08, 2022)
3-33092922-A-T		not specified	Uncertain significance (Jan 23, 2024)
3-33093113-G-T		not specified	Uncertain significance (Jan 23, 2024)
3-33093130-C-G		not specified	Uncertain significance (Feb 27, 2023)
3-33093235-T-C		not specified	Likely benign (Feb 15, 2023)
3-33093265-G-A		not specified	Uncertain significance (Jun 24, 2022)
3-33093351-G-A		not specified	Uncertain significance (May 24, 2023)
3-33093385-C-T		not specified	Likely benign (Dec 08, 2023)
3-33093400-G-C		not specified	Uncertain significance (Jun 07, 2023)
3-33093451-C-T		not specified	Uncertain significance (Feb 05, 2024)
3-33093474-G-A		not specified	Uncertain significance (Nov 05, 2021)
3-33093495-T-C		not specified	Uncertain significance (Dec 15, 2022)
3-33093568-C-T		not specified	Uncertain significance (Mar 29, 2022)
3-33093579-T-C		not specified	Uncertain significance (Aug 29, 2022)
3-33093582-T-C		not specified	Uncertain significance (Feb 06, 2023)
3-33093642-G-A		not specified	Uncertain significance (Nov 14, 2023)
3-33093672-A-G		not specified	Uncertain significance (Feb 12, 2024)
3-33093739-C-T		not specified	Uncertain significance (Oct 10, 2023)
3-33093753-C-T		not specified	Uncertain significance (Feb 28, 2024)
3-33093832-G-T		not specified	Uncertain significance (Jan 04, 2024)
3-33093916-C-T		not specified	Uncertain significance (Apr 25, 2023)
3-33093955-A-G		not specified	Uncertain significance (Feb 23, 2023)
3-33093957-G-T		not specified	Uncertain significance (Feb 13, 2023)
3-33093990-C-T		not specified	Uncertain significance (Nov 19, 2022)
3-33094023-A-G		not specified	Uncertain significance (Feb 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMPPE	protein_coding	protein_coding	ENST00000342462	1	6381

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000852	0.803	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	226	277	0.817	0.0000164	2932
Missense in Polyphen		61	88.924	0.68598		966
Synonymous	0.247	118	121	0.971	0.00000772	998
Loss of Function	1.10	6	9.69	0.619	4.14e-7	118

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000448	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.0869
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.46

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.362
• ghis: 0.399

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmppe

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: hydrolase activity;metal ion binding