LMNTD2

lamin tail domain containing 2

Basic information

Region (hg38): 11:554850-560738

Previous symbols: [ "C11orf35" ]

Links

ENSG00000185522 ∙ NCBI:256329 ∙ ∙ HGNC:28561 ∙ Uniprot:Q8IXW0 ∙ 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 LMNTD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LMNTD2 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				1	3	4
missense			87	10		97
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	87	11	3

Variants in LMNTD2

This is a list of pathogenic ClinVar variants found in the LMNTD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-554996-G-T		not specified	Uncertain significance (Feb 05, 2025)
11-554997-T-C		not specified	Uncertain significance (Nov 11, 2024)
11-554999-T-A		not specified	Uncertain significance (Jan 02, 2024)
11-555011-G-A		not specified	Uncertain significance (Dec 26, 2023)
11-555011-G-C		not specified	Uncertain significance (Sep 01, 2021)
11-555069-G-C		not specified	Uncertain significance (Mar 28, 2024)
11-555095-A-G		not specified	Uncertain significance (Nov 28, 2023)
11-555315-T-C		not specified	Uncertain significance (Feb 01, 2025)
11-555317-T-C			Benign (Sep 01, 2023)
11-555352-C-T		not specified	Uncertain significance (Oct 20, 2024)
11-555354-G-C		not specified	Uncertain significance (Mar 29, 2022)
11-555360-G-C		not specified	Uncertain significance (Jan 10, 2025)
11-555369-G-A		not specified	Uncertain significance (Oct 06, 2022)
11-555378-G-A		not specified	Uncertain significance (Nov 20, 2024)
11-555411-G-A		not specified	Uncertain significance (Jun 30, 2024)
11-555445-G-T		not specified	Uncertain significance (Jul 31, 2024)
11-555454-G-A		not specified	Uncertain significance (Jun 29, 2023)
11-555472-C-G		not specified	Uncertain significance (Jan 23, 2024)
11-555472-C-T		not specified	Uncertain significance (Jan 10, 2023)
11-555474-G-A		not specified	Uncertain significance (Mar 07, 2025)
11-555484-G-C		not specified	Uncertain significance (Apr 11, 2023)
11-555498-C-G		not specified	Uncertain significance (Sep 16, 2021)
11-555499-G-A		not specified	Uncertain significance (Mar 22, 2022)
11-555765-G-A		not specified	Uncertain significance (Dec 17, 2023)
11-555767-A-G		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LMNTD2	protein_coding	protein_coding	ENST00000329451	14	5925

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.79e-26	0.00000990	125234	0	161	125395	0.000642

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.16	406	345	1.18	0.0000204	3914
Missense in Polyphen		112	92.708	1.2081		1153
Synonymous	-2.14	185	151	1.22	0.00000913	1322
Loss of Function	-1.50	34	25.8	1.32	0.00000136	302

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00218	0.00211
Ashkenazi Jewish	0.00	0.00
East Asian	0.00138	0.00136
Finnish	0.0000951	0.0000925
European (Non-Finnish)	0.000503	0.000477
Middle Eastern	0.00138	0.00136
South Asian	0.000682	0.000654
Other	0.00102	0.000981

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.0670
• hipred: N
• hipred_score: 0.180
• ghis: 0.394

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Lmntd2