MTMR1
Basic information
Region (hg38): X:150692971-150765108
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTMR1 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 | 3 | |||||
missense | 25 | 26 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 1 | 1 | ||||
non coding | 9 | |||||
Total | 0 | 0 | 25 | 3 | 10 |
Variants in MTMR1
This is a list of pathogenic ClinVar variants found in the MTMR1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
X-150693550-C-A | not specified | Uncertain significance (Aug 02, 2021) | ||
X-150693570-G-A | not specified | Uncertain significance (Oct 12, 2021) | ||
X-150693582-C-G | not specified | Uncertain significance (Apr 19, 2024) | ||
X-150693596-G-C | Likely benign (Sep 01, 2022) | |||
X-150693651-C-A | not specified | Uncertain significance (Dec 27, 2022) | ||
X-150693741-A-C | Benign (Jun 19, 2021) | |||
X-150698971-CTTTG-C | Benign (Jun 20, 2021) | |||
X-150699265-T-A | not specified | Uncertain significance (Aug 10, 2021) | ||
X-150718584-C-T | Benign (Jun 19, 2021) | |||
X-150718626-C-G | not specified | Uncertain significance (Aug 16, 2022) | ||
X-150718858-C-T | Benign (Nov 12, 2018) | |||
X-150727244-A-T | not specified | Uncertain significance (Apr 06, 2022) | ||
X-150727547-G-A | Benign (Nov 12, 2018) | |||
X-150727727-G-A | not specified | Uncertain significance (Jul 19, 2022) | ||
X-150730140-A-G | not specified | Uncertain significance (Dec 14, 2021) | ||
X-150730534-G-T | not specified | Uncertain significance (Feb 27, 2023) | ||
X-150730566-T-A | not specified | Uncertain significance (Dec 28, 2022) | ||
X-150730573-A-C | not specified | Uncertain significance (Dec 28, 2023) | ||
X-150731555-C-T | not specified | Uncertain significance (May 14, 2024) | ||
X-150731569-G-T | not specified | Uncertain significance (Jan 08, 2024) | ||
X-150731603-C-T | not specified | Uncertain significance (Mar 06, 2023) | ||
X-150731781-A-G | Benign (Jun 19, 2021) | |||
X-150731903-T-G | Benign (Nov 12, 2018) | |||
X-150732542-G-C | not specified | Uncertain significance (May 17, 2023) | ||
X-150732620-C-T | not specified | Uncertain significance (Jun 29, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
MTMR1 | protein_coding | protein_coding | ENST00000544228 | 15 | 72142 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.998 | 0.00240 | 123989 | 0 | 2 | 123991 | 0.00000807 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.02 | 150 | 238 | 0.631 | 0.0000189 | 4364 |
Missense in Polyphen | 23 | 64.083 | 0.35891 | 1054 | ||
Synonymous | 0.00586 | 94 | 94.1 | 0.999 | 0.00000805 | 1280 |
Loss of Function | 4.41 | 2 | 26.5 | 0.0755 | 0.00000223 | 420 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.0000628 | 0.0000462 |
European (Non-Finnish) | 0.00 | 0.00 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000566 | 0.0000345 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Lipid phosphatase that has high specificity for phosphatidylinositol 3-phosphate and has no activity with phosphatidylinositol 4-phosphate, phosphatidylinositol (4,5)- bisphosphate and phosphatidylinositol (3,4,5)-trisphosphate (PubMed:11733541, PubMed:27018598). Activity with phosphatidylinositol (3,5)-bisphosphate is controversial; it has been shown by PubMed:27018598, while PubMed:11733541 find no activity with this substrate. {ECO:0000269|PubMed:11733541, ECO:0000269|PubMed:27018598}.;
- Pathway
- Inositol phosphate metabolism - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Metabolism of lipids;Metabolism;Nicotinate Nicotinamide metabolism;Synthesis of PIPs at the plasma membrane;PI Metabolism;Phospholipid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.176
Intolerance Scores
- loftool
- 0.175
- rvis_EVS
- -0.09
- rvis_percentile_EVS
- 46.74
Haploinsufficiency Scores
- pHI
- 0.400
- hipred
- Y
- hipred_score
- 0.696
- ghis
- 0.520
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.469
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Mtmr1
- Phenotype
- normal phenotype;
Gene ontology
- Biological process
- phosphatidylinositol biosynthetic process;peptidyl-tyrosine dephosphorylation;phosphatidylinositol dephosphorylation;regulation of phosphatidylinositol dephosphorylation
- Cellular component
- cytoplasm;cytosol;plasma membrane
- Molecular function
- phosphatidylinositol-3-phosphatase activity;protein tyrosine phosphatase activity;protein homodimerization activity;phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity