GML
protein-codingglycosylphosphatidylinositol anchored molecule like, the group of LY6/PLAUR domain containing
Gene summary
Predicted to be involved in DNA damage response, signal transduction by p53 class mediator; apoptotic process; and negative regulation of cell population proliferation. Predicted to be located in plasma membrane. Predicted to be extrinsic component of membrane. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~82.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to GML variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002066.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 20 | 1 | 21 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 20 | 1 | 1 | 22 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002057.1 | 3 | MANE Select | |
| Ensembl | ENSP00000220940.1 | 3 | MANE Select | |
| Ensembl | ENSP00000430799.1 | 4 | Standard | |
| Ensembl | ENSP00000773172.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Cellular response to heat stress
- HSF1 activation
- Attenuation phase
- HSF1-dependent transactivation
- Regulation of HSF1-mediated heat shock response
Biological Process
- apoptotic process
- DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
- negative regulation of cell population proliferation
Cellular Component
- plasma membrane
- extrinsic component of membrane
- anchored component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000220940
- Coding exons
- 3
- Length
- 82260
- Individuals with no LoFs
- 125223
- Homozygous LoFs
- 6
- Heterozygous LoFs
- 508
- Defined
- 125737
- p
- 0.00205
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.00207 | 91 | 91.1 | 0.999 | 0.00000464 | 1043 |
| Missense (PolyPhen) | 23 | 23.852 | 0.96429 | 311 | ||
| Synonymous | 1.44 | 22 | 32.4 | 0.678 | 0.00000175 | 301 |
| Loss of Function | 1.07 | 1 | 3.00 | 0.333 | 1.26e-7 | 37 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.028 | 0.028 | notable |
| Latino/Admixed American | 0.0014 | 0.0014 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000057 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000035 | 0.000035 | rare |
| South Asian | 0.00035 | 0.00033 | rare |
| Other | 0.00065 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May play a role in the apoptotic pathway or cell-cycle regulation induced by p53/TP53 after DNA damage.;
Recessive Scores
- pRec
- 0.0876
Intolerance Scores
- LoFtool
- 0.761
- RVIS EVS
- 0.55
- RVIS percentile EVS
- 81.38
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.101
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |