LMNTD1

lamin tail domain containing 1

Basic information

Region (hg38): 12:25409307-25648579

Previous symbols: [ "IFLTD1" ]

Links

ENSG00000152936 ∙ NCBI:160492 ∙ OMIM:617254 ∙ HGNC:26683 ∙ Uniprot:Q8N9Z9 ∙ 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 LMNTD1 gene.

• not_specified (47 variants)
• Preeclampsia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LMNTD1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001145728.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			44	3		47
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	44	3	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LMNTD1	protein_coding	protein_coding	ENST00000458174	8	239273

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.09e-10	0.306	125670	0	58	125728	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.809	176	209	0.843	0.0000104	2655
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000660	0.000660
Ashkenazi Jewish	0.00151	0.00149
East Asian	0.0000674	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.0000674	0.0000544
South Asian	0.00	0.00
Other	0.000833	0.000815

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0747

Intolerance Scores

• rvis_EVS: 1.64
• rvis_percentile_EVS: 96.15

Haploinsufficiency Scores

• pHI: 0.147
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Lmntd1

Gene ontology

• Biological process: cell population proliferation
• Cellular component: nuclear envelope;cytoplasm;intermediate filament
• Molecular function: structural molecule activity