LMNTD2

Summary

LMNTD2 (lamin tail domain containing 2, HGNC:28561) is a protein-coding gene on chromosome 11p15.5, encoding Lamin tail domain-containing protein 2 (Q8IXW0).

Predicted to be a structural constituent of chromatin. Predicted to act upstream of or within positive regulation of mRNA splicing, via spliceosome. Predicted to be active in lamin filament.

Source: NCBI Gene 256329 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 198 total
• MANE Select transcript: NM_173573

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28561
Approved symbol	LMNTD2
Name	lamin tail domain containing 2
Location	11p15.5
Locus type	gene with protein product
Status	Approved
Aliases	MGC35138
Ensembl gene	ENSG00000185522
Ensembl biotype	protein_coding
Entrez	256329

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 5 protein_coding, 2 retained_intron

ENST00000329451, ENST00000441853, ENST00000469990, ENST00000486629, ENST00000492515, ENST00000886189, ENST00000886190

RefSeq mRNA: 1 — MANE Select: NM_173573 NM_173573

CCDS: CCDS7701

Canonical transcript exons

ENST00000329451 — 14 exons

Exon	Start	End
ENSE00001295593	555734	555930
ENSE00001295620	558614	558766
ENSE00001296983	560683	560738
ENSE00001298372	556192	556375
ENSE00001306520	556492	556588
ENSE00001306818	557572	557640
ENSE00001312942	555305	555503
ENSE00001316541	558161	558248
ENSE00001328866	557884	558039
ENSE00001330778	556835	557097
ENSE00001911819	554850	555111
ENSE00003479106	555996	556115
ENSE00003480240	558856	558979
ENSE00003788379	557399	557487

Expression profiles

Bgee: expression breadth ubiquitous, 129 present calls, max score 92.41.

FANTOM5 (CAGE): breadth broad, TPM avg 1.0611 / max 24.8347, expressed in 648 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
117778	1.0471	647
117777	0.0140	3

Top tissues by expression

132 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	92.41	gold quality
right lobe of liver	UBERON:0001114	89.51	gold quality
right testis	UBERON:0004534	89.15	gold quality
left testis	UBERON:0004533	88.19	gold quality
metanephros cortex	UBERON:0010533	87.96	gold quality
testis	UBERON:0000473	87.45	gold quality
cortex of kidney	UBERON:0001225	85.38	gold quality
right hemisphere of cerebellum	UBERON:0014890	85.38	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.32	gold quality
mucosa of transverse colon	UBERON:0004991	84.88	gold quality
lower esophagus mucosa	UBERON:0035834	84.85	gold quality
cerebellar cortex	UBERON:0002129	84.02	gold quality
cerebellar hemisphere	UBERON:0002245	83.98	gold quality
cerebellum	UBERON:0002037	83.94	gold quality
pituitary gland	UBERON:0000007	83.80	gold quality
body of pancreas	UBERON:0001150	82.72	gold quality
right lung	UBERON:0002167	82.20	gold quality
left lobe of thyroid gland	UBERON:0001120	82.13	gold quality
thyroid gland	UBERON:0002046	81.58	gold quality
liver	UBERON:0002107	81.53	gold quality
right lobe of thyroid gland	UBERON:0001119	81.33	gold quality
adenohypophysis	UBERON:0002196	81.33	gold quality
granulocyte	CL:0000094	80.52	gold quality
skin of abdomen	UBERON:0001416	80.43	gold quality
adult mammalian kidney	UBERON:0000082	80.28	gold quality
zone of skin	UBERON:0000014	79.76	gold quality
skin of leg	UBERON:0001511	79.57	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	79.15	gold quality
body of stomach	UBERON:0001161	78.40	gold quality
upper lobe of left lung	UBERON:0008952	78.37	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.97

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

3 targeting LMNTD2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-659-3P	99.85	70.69	1620
HSA-MIR-4717-5P	98.19	67.97	894

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Lmntd2	ENSMUSG00000025500
rattus_norvegicus	Lmntd2	ENSRNOG00000017050
caenorhabditis_elegans		WBGENE00044296

Protein

Protein identifiers

Lamin tail domain-containing protein 2 — Q8IXW0 (reviewed: Q8IXW0)

All UniProt accessions (3): Q8IXW0, C9JV74, E9PJR3

RefSeq proteins (1): NP_775844* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001322	Lamin_tail_dom	Domain
IPR036415	Lamin_tail_dom_sf	Homologous_superfamily
IPR052877	Lamin_tail_domain	Family

Pfam: PF00932

UniProt features (13 total): compositionally biased region 6, region of interest 3, chain 1, domain 1, sequence variant 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IXW0-F1	55.68	0.15

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 67 (showing top): RNGTGGGC_UNKNOWN, AREB6_03, AREB6_01, HNF1_Q6, EGR1_01, GOCC_NUCLEAR_ENVELOPE, GOCC_INTERMEDIATE_FILAMENT_CYTOSKELETON, GOCC_NUCLEAR_PERIPHERY, GOMF_STRUCTURAL_MOLECULE_ACTIVITY, GOCC_ORGANELLE_ENVELOPE, KOHOUTEK_CCNT2_TARGETS, GOCC_NUCLEAR_LAMINA, LIM_MAMMARY_LUMINAL_MATURE_UP, GOCC_SUPRAMOLECULAR_COMPLEX, GOCC_POLYMERIC_CYTOSKELETAL_FIBER

GO Biological Process (0):

GO Molecular Function (2): structural constituent of chromatin (GO:0030527), protein binding (GO:0005515)

GO Cellular Component (1): lamin filament (GO:0005638)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
chromatin	1
structural molecule activity	1
binding	1
nuclear lamina	1
intermediate filament	1

Protein interactions and networks

STRING

436 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LMNTD2	PRR33	A8MZF0	506
LMNTD2	SNX22	Q96L94	450
LMNTD2	RHPN1	Q8TCX5	432
LMNTD2	HOATZ	Q6PI97	427
LMNTD2	PPP1R16A	Q96I34	410
LMNTD2	CLEC18A	A5D8T8	390
LMNTD2	SPAG8	Q99932	357
LMNTD2	TTC39C	Q8N584	349
LMNTD2	OLFML2A	Q68BL7	339
LMNTD2	HSD11B1	P28845	336
LMNTD2	ERMN	Q8TAM6	330
LMNTD2	ABTB1	Q969K4	324
LMNTD2	NXT2	Q9NPJ8	321
LMNTD2	CCT6B	Q92526	320
LMNTD2	PTGDR	Q13258	311
LMNTD2	A0A024R161	A0A024R161	311

IntAct

61 interactions, top by confidence:

A	B	Type	Score
LMNTD2	TNS2	psi-mi:“MI:0915”(physical association)	0.560
LMNTD2	TRAF2	psi-mi:“MI:0915”(physical association)	0.560
LMNTD2	KRTAP5-6	psi-mi:“MI:0915”(physical association)	0.560
TNS2	LMNTD2	psi-mi:“MI:0915”(physical association)	0.560
CYSRT1	LMNTD2	psi-mi:“MI:0915”(physical association)	0.560
TRAF2	LMNTD2	psi-mi:“MI:0915”(physical association)	0.560
KRTAP5-6	LMNTD2	psi-mi:“MI:0915”(physical association)	0.560
LMNTD2	KRTAP9-2	psi-mi:“MI:0915”(physical association)	0.560
KRTAP12-3	LMNTD2	psi-mi:“MI:0915”(physical association)	0.560
RBMY1A1	LMNTD2	psi-mi:“MI:0915”(physical association)	0.560
KRT31	LMNTD2	psi-mi:“MI:0915”(physical association)	0.560
NOTCH2NLC	LMNTD2	psi-mi:“MI:0915”(physical association)	0.560
KRTAP5-2	LMNTD2	psi-mi:“MI:0915”(physical association)	0.560
LMNTD2	KRTAP9-3	psi-mi:“MI:0915”(physical association)	0.560
KHDRBS3	LMNTD2	psi-mi:“MI:0915”(physical association)	0.560
KRT27	LMNTD2	psi-mi:“MI:0915”(physical association)	0.560
TRAF1	LMNTD2	psi-mi:“MI:0915”(physical association)	0.560
KHDRBS2	LMNTD2	psi-mi:“MI:0915”(physical association)	0.560
FBLN1	LMNTD2	psi-mi:“MI:0915”(physical association)	0.560
C3orf62	LMNTD2	psi-mi:“MI:0915”(physical association)	0.560
INCA1	LMNTD2	psi-mi:“MI:0915”(physical association)	0.560
LMNTD2	MID2	psi-mi:“MI:0915”(physical association)	0.560
TBC1D25	LMNTD2	psi-mi:“MI:0915”(physical association)	0.560
LMNTD2	KRTAP9-2	psi-mi:“MI:0915”(physical association)	0.000
LMNTD2	KRTAP12-3	psi-mi:“MI:0915”(physical association)	0.000
LMNTD2	RBMY1A1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (19): LMNTD2 (Two-hybrid), LMNTD2 (Two-hybrid), LMNTD2 (Two-hybrid), LMNTD2 (Two-hybrid), LMNTD2 (Two-hybrid), LMNTD2 (Two-hybrid), LMNTD2 (Two-hybrid), LMNTD2 (Two-hybrid), C3orf62 (Two-hybrid), INCA1 (Two-hybrid), CYSRT1 (Two-hybrid), KRTAP9-3 (Two-hybrid), KRTAP12-3 (Two-hybrid), KRTAP5-2 (Two-hybrid), RBMY1A1 (Two-hybrid)

ESM2 similar proteins: A0A1B0GVZ6, A5D7I0, A6H7B4, A6NDZ8, A6NE82, A6NJ08, A6NJB7, A6NJI1, A6NL46, A6QP24, A8MUA0, A8MUI8, A8MV72, A8MX80, B2RW88, O94850, P0C6A0, P24097, P50617, Q0P5M0, Q0VD86, Q2KIL8, Q3B8N5, Q3SY00, Q3SYA9, Q3UN58, Q5BMD4, Q5JTZ5, Q5RBE4, Q5VZ46, Q66MI6, Q68US1, Q6GQV0, Q6PAC4, Q80TS7, Q80VY2, Q8BFY7, Q8BII1, Q8IXW0, Q8K2F3

Diamond homologs: Q0VET5, Q8IXW0, Q9D4C1, A0A125S9M5, P02545, P08928, P11048, P13648, P14731, P14732, P21619, P48678, P48679, Q03252, Q4R899, Q8N9Z9

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 20 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Keratinization	7	27.9×	7e-08

Disease & clinical

Clinical variants and AI predictions

ClinVar

198 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	158
Likely benign	17
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

2320 predictions. Top by Δscore:

Variant	Effect	Δscore
11:556371:TCGGG:T	acceptor_gain	1.0000
11:556372:CGGG:C	acceptor_gain	1.0000
11:556372:CGGGC:C	acceptor_gain	1.0000
11:556373:GGG:G	acceptor_gain	1.0000
11:556374:GG:G	acceptor_gain	1.0000
11:556376:C:CC	acceptor_gain	1.0000
11:556377:T:A	acceptor_loss	1.0000
11:556488:TTACC:T	donor_loss	1.0000
11:556489:TACC:T	donor_loss	1.0000
11:556490:ACC:A	donor_loss	1.0000
11:556491:C:CG	donor_loss	1.0000
11:556491:CCT:C	donor_gain	1.0000
11:557397:A:AC	donor_gain	1.0000
11:557398:C:CC	donor_gain	1.0000
11:557879:CTCA:C	donor_loss	1.0000
11:557881:CAC:C	donor_loss	1.0000
11:557882:A:AC	donor_gain	1.0000
11:557882:ACCT:A	donor_gain	1.0000
11:557883:C:A	donor_loss	1.0000
11:557883:C:CC	donor_gain	1.0000
11:557883:CCTC:C	donor_gain	1.0000
11:557885:T:TA	donor_gain	1.0000
11:557958:T:TA	donor_gain	1.0000
11:558160:CCCA:C	donor_gain	1.0000
11:558163:A:AC	donor_gain	1.0000
11:558164:C:CC	donor_gain	1.0000
11:558615:T:TA	donor_gain	1.0000
11:558638:T:TA	donor_gain	1.0000
11:558641:T:TA	donor_gain	1.0000
11:558854:A:AC	donor_gain	1.0000

AlphaMissense

4053 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:556232:A:G	F406S	0.992
11:556114:A:T	V420D	0.987
11:556231:G:C	F406L	0.987
11:556231:G:T	F406L	0.987
11:556233:A:G	F406L	0.987
11:556232:A:C	F406C	0.982
11:556322:A:G	I376T	0.980
11:557463:A:G	W217R	0.977
11:557463:A:T	W217R	0.977
11:556315:G:C	N378K	0.975
11:556315:G:T	N378K	0.975
11:557890:A:C	S183R	0.975
11:557890:A:T	S183R	0.975
11:557892:T:G	S183R	0.975
11:555844:G:C	F488L	0.973
11:555844:G:T	F488L	0.973
11:555846:A:G	F488L	0.973
11:555922:A:C	S462R	0.973
11:555922:A:T	S462R	0.973
11:555924:T:G	S462R	0.973
11:556328:A:T	V374D	0.973
11:557925:A:G	W172R	0.973
11:557925:A:T	W172R	0.973
11:556322:A:C	I376S	0.971
11:555037:G:C	F616L	0.969
11:555037:G:T	F616L	0.969
11:555039:A:G	F616L	0.969
11:556196:A:T	V418D	0.969
11:556322:A:T	I376N	0.967
11:556325:C:G	R375P	0.967

dbSNP variants (sampled 300 via entrez): RS1000454829 (11:554607 G>A), RS1000856296 (11:562111 C>T), RS1001272694 (11:556153 G>A), RS1001576130 (11:559692 G>A), RS1001759149 (11:561199 G>A,C,T), RS1002169199 (11:558839 C>G), RS1002277856 (11:557853 T>C), RS1002278256 (11:555453 C>G,T), RS1002403968 (11:554370 G>C,T), RS1002404372 (11:555564 C>G,T), RS1002498488 (11:556167 G>A,T), RS1002969970 (11:561597 C>A), RS1003025996 (11:560003 C>T), RS1003490315 (11:557302 C>T), RS1003877969 (11:559723 G>A,T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:616345

GenCC curated gene-disease

Mondo (1): immunodeficiency 39 (MONDO:0014597)

Orphanet (1): Predisposition to severe viral infection due to IRF7 deficiency (Orphanet:574918)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST003155_11	Systemic lupus erythematosus	9.000000e-10

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
afuresertib	increases expression	1
bisphenol F	affects cotreatment, increases methylation	1
bisphenol A	increases methylation, decreases methylation, affects cotreatment	1
butyraldehyde	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
Sunitinib	decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Acetaminophen	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	affects methylation	1
Cisplatin	affects cotreatment, increases expression	1
Estradiol	decreases expression	1
Oxygen	increases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Triclosan	increases expression	1
Valproic Acid	increases methylation	1
Okadaic Acid	decreases expression	1
Acrylamide	decreases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.