LMNTD1
protein-codinglamin tail domain containing 1
Gene summary
Predicted to act upstream of or within cell population proliferation. Predicted to be located in intermediate filament and nucleus. Predicted to be active in cytoplasm and nuclear envelope. [provided by Alliance of Genome Resources, Jul 2025]
- IFLTD1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~239.3 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 LMNTD1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001145728.2. 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 | 0 | |||||
| missense | 53 | 3 | 56 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 55 | 3 | 0 | 58 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001139200.1 | 8 | MANE Select | |
| Ensembl | ENSP00000407353.2 | 8 | MANE Select | |
| RefSeq | NP_001139199.1 | 7 | Standard | |
| RefSeq | NP_001139201.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- cell population proliferation
Molecular Function
- structural molecule activity
Cellular Component
- nuclear envelope
- cytoplasm
- intermediate filament
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000458174
- Coding exons
- 8
- Length
- 239273
- Individuals with no LoFs
- 125670
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 58
- Defined
- 125728
- p
- 0.000231
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.809 | 176 | 209 | 0.843 | 0.0000104 | 2655 |
| Missense (PolyPhen) | 46 | 56.403 | 0.81557 | 792 | ||
| Synonymous | 0.0419 | 74 | 74.5 | 0.994 | 0.00000400 | 767 |
| Loss of Function | 0.924 | 18 | 22.8 | 0.791 | 0.00000120 | 275 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.00041 | 0.00040 | rare |
| Ashkenazi Jewish | 0.0015 | 0.0015 | notable |
| East Asian | 0.000067 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00017 | 0.00017 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00083 | 0.00082 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.0747
Intolerance Scores
- RVIS EVS
- 1.64
- RVIS percentile EVS
- 96.15
Essentials
- Essential (gene trap)
- N