LMNTD2

protein-coding

lamin tail domain containing 2

Gene summary

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. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C11orf35

MANE transcript

NM_173573.3

Inheritance

—

ClinVar variants

U:168B:21

Top phenotype

Primary ciliary dyskinesia

gnomAD constraint

pLI —, LoF o/e 1.32

Max pathogenic AF

—

Genomic locus

chr11:554,850-560,738

External References & Databases

Ensembl (ENSG00000185522)

Transcript & Mutation Effects

hg38 • Region Span ~5.9 kb

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GenCC 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 LMNTD2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 175

not providedTotal: 6

Primary ciliary dyskinesiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173573.3. 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			5 clinvar	2 clinvar	3 clinvar	10
missense			160 clinvar	16 clinvar		176
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	168	18	3	189

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173573.3	RefSeq	NP_775844.2	14	MANE Select
ENST00000329451.8	Ensembl	ENSP00000331167.3	14	MANE Select
ENST00000441853.5	Ensembl	ENSP00000393529.1	8	Standard
ENST00000486629.1	Ensembl	ENSP00000435529.1	6	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000329451
Coding exons: 14
Length: 5925
Individuals with no LoFs: 125234
Homozygous LoFs: 0
Heterozygous LoFs: 161
Defined: 125395
p: 0.000642

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.16	406	345	1.18	0.0000204	3914
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0011	0.00099	notable
Latino/Admixed American	0.0011	0.0011	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0014	0.0014	notable
Finnish	0.000095	0.000092	rare
European (Non-Finnish)	0.00050	0.00048	rare
South Asian	0.00068	0.00065	rare
Other	0.0010	0.00098	notable

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (gene trap): N