LSM14B

Summary

LSM14B (LSM family member 14B, HGNC:15887) is a protein-coding gene on chromosome 20q13.33, encoding Protein LSM14 homolog B (Q9BX40). mRNA-binding protein essential for female fertility, oocyte meiotic maturation and the assembly of MARDO (mitochondria-associated ribonucleoprotein domain), a membraneless compartment that stores maternal mRNAs in oocytes.

Enables RNA binding activity. Predicted to be involved in several processes, including maternal mRNA clearance; meiotic cell cycle process involved in oocyte maturation; and ovarian follicle development. Predicted to be located in cytoplasmic ribonucleoprotein granule. Predicted to be part of ribonucleoprotein complex.

Source: NCBI Gene 149986 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 53 total
• MANE Select transcript: NM_144703

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:15887
Approved symbol	LSM14B
Name	LSM family member 14B
Location	20q13.33
Locus type	gene with protein product
Status	Approved
Aliases	FT005, bA11M20.3, FLJ25473, LSM13, RAP55B
Ensembl gene	ENSG00000149657
Ensembl biotype	protein_coding
OMIM	620689
Entrez	149986

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 8 protein_coding

ENST00000279068, ENST00000279069, ENST00000361670, ENST00000370915, ENST00000400318, ENST00000886858, ENST00000924405, ENST00000924406

RefSeq mRNA: 1 — MANE Select: NM_144703 NM_144703

CCDS: CCDS46626

Canonical transcript exons

ENST00000279068 — 9 exons

Exon	Start	End
ENSE00000991849	62129785	62129952
ENSE00000991850	62130219	62130296
ENSE00001335295	62134163	62135374
ENSE00001747199	62133290	62133475
ENSE00001813884	62122475	62122793
ENSE00002711126	62130530	62130691
ENSE00003575228	62124617	62124780
ENSE00003674050	62126304	62126439
ENSE00003786220	62131356	62131506

Expression profiles

Bgee: expression breadth ubiquitous, 226 present calls, max score 98.06.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 59.8453 / max 295.2209, expressed in 1813 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
185699	59.8121	1813
185701	0.0226	3
185700	0.0106	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	98.06	gold quality
cortical plate	UBERON:0005343	96.77	gold quality
ganglionic eminence	UBERON:0004023	96.27	gold quality
male germ cell	CL:0000015	95.98	gold quality
cerebellar hemisphere	UBERON:0002245	95.09	gold quality
cerebellar cortex	UBERON:0002129	95.02	gold quality
ventricular zone	UBERON:0003053	94.99	gold quality
right hemisphere of cerebellum	UBERON:0014890	94.80	gold quality
right testis	UBERON:0004534	94.56	gold quality
left testis	UBERON:0004533	94.50	gold quality
cerebellum	UBERON:0002037	93.51	gold quality
prefrontal cortex	UBERON:0000451	93.14	gold quality
hindlimb stylopod muscle	UBERON:0004252	93.12	gold quality
gastrocnemius	UBERON:0001388	92.88	gold quality
right ovary	UBERON:0002118	92.39	gold quality
left ovary	UBERON:0002119	92.38	gold quality
testis	UBERON:0000473	92.25	gold quality
muscle of leg	UBERON:0001383	92.22	gold quality
right frontal lobe	UBERON:0002810	92.03	gold quality
apex of heart	UBERON:0002098	91.87	gold quality
monocyte	CL:0000576	91.83	gold quality
anterior cingulate cortex	UBERON:0009835	91.79	gold quality
cingulate cortex	UBERON:0003027	91.73	gold quality
mononuclear cell	CL:0000842	91.56	gold quality
leukocyte	CL:0000738	91.36	gold quality
body of uterus	UBERON:0009853	91.23	gold quality
skin of leg	UBERON:0001511	91.13	gold quality
Brodmann (1909) area 9	UBERON:0013540	91.11	gold quality
skin of abdomen	UBERON:0001416	90.83	gold quality
heart left ventricle	UBERON:0002084	90.24	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	2.99

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

71 targeting LSM14B, 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-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-590-3P	99.96	74.34	6478
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-302A-3P	99.89	71.23	1777
HSA-MIR-302B-3P	99.89	71.23	1777
HSA-MIR-302C-3P	99.89	71.20	1778
HSA-MIR-302D-3P	99.89	71.25	1777
HSA-MIR-4496	99.88	68.89	2236
HSA-MIR-3065-3P	99.87	70.25	1407
HSA-MIR-659-3P	99.85	70.69	1620
HSA-MIR-576-5P	99.84	70.46	2582
HSA-MIR-489-3P	99.80	66.46	839
HSA-MIR-323A-3P	99.79	70.30	1739
HSA-MIR-5002-5P	99.76	70.84	1763
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-6752-3P	99.72	66.71	1587
HSA-MIR-1283	99.69	72.42	3009
HSA-MIR-519A-3P	99.67	71.67	1868
HSA-MIR-519B-3P	99.67	71.67	1868

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	lsm14b	ENSDARG00000025386
mus_musculus	Lsm14b	ENSMUSG00000039108
rattus_norvegicus	Lsm14b	ENSRNOG00000054557
drosophila_melanogaster	tral	FBGN0041775
caenorhabditis_elegans	car-1	WBGENE00012484

Paralogs (1): LSM14A (ENSG00000257103)

Protein

Protein identifiers

Protein LSM14 homolog B — Q9BX40 (reviewed: Q9BX40)

Alternative names: RNA-associated protein 55B

All UniProt accessions (5): Q9BX40, A0A0C4DFV2, Q5TBP9, Q5TBQ0, Q5TBQ1

UniProt curated annotations — full annotation on UniProt →

Function. mRNA-binding protein essential for female fertility, oocyte meiotic maturation and the assembly of MARDO (mitochondria-associated ribonucleoprotein domain), a membraneless compartment that stores maternal mRNAs in oocytes. Ensures the proper accumulation and clearance of mRNAs essential for oocyte meiotic maturation and the normal progression from Meiosis I to Meiosis II in oocytes. Promotes the translation of some oogenesis-related mRNAs. Regulates the expression and/or localization of some key P-body proteins in oocytes. Essential for the assembly of the primordial follicle in the ovary.

Subunit / interactions. Component of a ribonucleoprotein (RNP) complex. Interacts with DDX6.

Subcellular location. Cytoplasm. Cytoplasmic ribonucleoprotein granule.

Similarity. Belongs to the LSM14 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9BX40-1	1	yes
Q9BX40-2	2
Q9BX40-3	3

RefSeq proteins (1): NP_653304* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010920	LSM_dom_sf	Homologous_superfamily
IPR019050	FDF_dom	Domain
IPR025609	Lsm14-like_N	Domain
IPR025761	FFD_box	Domain
IPR025762	DFDF	Domain
IPR025768	TFG_box	Domain
IPR047575	Sm	Domain

Pfam: PF09532, PF12701

UniProt features (28 total): modified residue 8, splice variant 5, compositionally biased region 3, sequence conflict 3, domain 2, region of interest 2, short sequence motif 2, initiator methionine 1, chain 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BX40-F1	63.00	0.19

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (9): 2, 106, 115, 154, 165, 329, 349, 351, 248

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 132 (showing top): GOZGIT_ESR1_TARGETS_DN, GOBP_OOGENESIS, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, PATIL_LIVER_CANCER, GOBP_TRANSLATION, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, GOBP_ANATOMICAL_STRUCTURE_MATURATION, GOBP_OVARIAN_FOLLICLE_DEVELOPMENT, GOBP_REPRODUCTIVE_SYSTEM_DEVELOPMENT, GOBP_CELL_MATURATION, GOBP_ORGANELLE_ASSEMBLY, GOBP_FEMALE_SEX_DIFFERENTIATION, MCBRYAN_PUBERTAL_BREAST_5_6WK_UP, GOBP_CELLULAR_PROCESS_INVOLVED_IN_REPRODUCTION_IN_MULTICELLULAR_ORGANISM, GOBP_OOCYTE_MATURATION

GO Biological Process (8): ovarian follicle development (GO:0001541), regulation of translation (GO:0006417), oogenesis (GO:0048477), membraneless organelle assembly (GO:0140694), maternal mRNA clearance (GO:0141065), meiotic cell cycle process involved in oocyte maturation (GO:1903537), cell differentiation (GO:0030154), meiotic cell cycle (GO:0051321)

GO Molecular Function (3): RNA binding (GO:0003723), mRNA binding (GO:0003729), protein binding (GO:0005515)

GO Cellular Component (3): cytoplasmic ribonucleoprotein granule (GO:0036464), ribonucleoprotein complex (GO:1990904), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
female gonad development	1
anatomical structure development	1
translation	1
post-transcriptional regulation of gene expression	1
regulation of protein metabolic process	1
germ cell development	1
female gamete generation	1
organelle assembly	1
mRNA catabolic process	1
maternal-to-zygotic transition of gene expression	1
oocyte maturation	1
meiotic cell cycle process	1
cellular developmental process	1
cell cycle	1
sexual reproduction	1
reproductive process	1
meiotic nuclear division	1
nucleic acid binding	1
RNA binding	1
binding	1
cytoplasm	1
ribonucleoprotein granule	1
protein-containing complex	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1464 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LSM14B	EIF4E1B	A6NMX2	787
LSM14B	PATL2	C9JE40	786
LSM14B	EDC3	Q96F86	784
LSM14B	EIF4ENIF1	Q9NRA8	725
LSM14B	LSM1	O15116	645
LSM14B	DDX6	P26196	644
LSM14B	PABPC1L	Q4VXU2	616
LSM14B	CPEB1	Q9BZB8	609
LSM14B	ARHGEF10L	Q9HCE6	596
LSM14B	PATL1	Q86TB9	586
LSM14B	NUFIP2	Q7Z417	575
LSM14B	LSM12	Q3MHD2	545
LSM14B	LSM4	Q9Y4Z0	534
LSM14B	XRN1	Q8IZH2	527
LSM14B	DCP1B	Q8IZD4	526

IntAct

76 interactions, top by confidence:

A	B	Type	Score
DDX6	RPS3	psi-mi:“MI:0915”(physical association)	0.690
C1QBP	DDX6	psi-mi:“MI:0915”(physical association)	0.620
DDX6	RPLP0	psi-mi:“MI:0915”(physical association)	0.620
DDX6	HSP90AA1	psi-mi:“MI:0915”(physical association)	0.540
SMC1A	PDS5B	psi-mi:“MI:0914”(association)	0.530
MAPT	KIF2A	psi-mi:“MI:0914”(association)	0.530
LSM14B	SEMG1	psi-mi:“MI:0914”(association)	0.530
BHLHA15	RPLP0	psi-mi:“MI:0914”(association)	0.530
CLEC3A	ZZEF1	psi-mi:“MI:0914”(association)	0.530
BHLHA15	YBX3	psi-mi:“MI:0914”(association)	0.530
DDX6	MCRIP1	psi-mi:“MI:0914”(association)	0.510
C1QBP	RPS3	psi-mi:“MI:0915”(physical association)	0.400
EIF4ENIF1	RPLP0	psi-mi:“MI:0915”(physical association)	0.400
EIF4ENIF1	PABPC1	psi-mi:“MI:0915”(physical association)	0.400
EIF4ENIF1	MCRIP1	psi-mi:“MI:0915”(physical association)	0.400
LSM14B	NCBP3	psi-mi:“MI:0915”(physical association)	0.400
PHF8	MACROH2A1	psi-mi:“MI:0914”(association)	0.350
HUWE1	NCOA4	psi-mi:“MI:0914”(association)	0.350
Iffo2	TAGLN2	psi-mi:“MI:0914”(association)	0.350
C1qbp		psi-mi:“MI:0914”(association)	0.350
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
PB2	SEC16A	psi-mi:“MI:0914”(association)	0.350
NS1	ESYT2	psi-mi:“MI:0914”(association)	0.350
MAPT	C11orf98	psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
CLEC3A	ZNF593	psi-mi:“MI:0914”(association)	0.350

BioGRID (146): SEMG2 (Affinity Capture-MS), SEMG1 (Affinity Capture-MS), SIRT3 (Affinity Capture-MS), ICK (Affinity Capture-MS), LSM14B (Affinity Capture-MS), LSM14B (Affinity Capture-MS), LSM14B (Affinity Capture-MS), LSM14B (Proximity Label-MS), LSM14B (Affinity Capture-MS), LSM14B (Affinity Capture-MS), LSM14B (Affinity Capture-MS), LSM14B (Affinity Capture-MS), LSM14B (Affinity Capture-MS), LSM14B (Affinity Capture-MS), LSM14B (Affinity Capture-MS)

ESM2 similar proteins: A0A8M2, A0JMU8, A1L1K8, A5D7H5, B9DFV2, E1BUG7, F4JP52, G1SW77, G3X9Z4, O08719, O15234, O94913, Q0V898, Q1LVV0, Q2T9I5, Q32NW2, Q3MHF8, Q498K9, Q566L7, Q5CZI8, Q5JVS0, Q5R4R4, Q5T8P6, Q5TYQ8, Q659C4, Q68FI1, Q6AXS5, Q6NVR8, Q6NZN0, Q6PKG0, Q8AVJ2, Q8CGC4, Q8K2F8, Q8K3W3, Q8K3X0, Q8NC51, Q8ND56, Q91W18, Q91W39, Q96D71

Diamond homologs: A0A8M2, P45978, Q3MHF8, Q498K9, Q566L7, Q5R4R4, Q68FI1, Q6NVR8, Q8AVJ2, Q8CGC4, Q8K2F8, Q8ND56, Q9BX40, Q9C658, Q9FH77, Q9HGL3, Q9XW17, Q9YH12

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 90 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.

GO biological processes:

GO term	Partners	Fold	FDR
negative regulation of translation	7	18.1×	7e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	39
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1859 predictions. Top by Δscore:

Variant	Effect	Δscore
20:62122789:CAAAG:C	donor_loss	1.0000
20:62122790:AAAGG:A	donor_loss	1.0000
20:62122791:AAGGT:A	donor_loss	1.0000
20:62122792:AGG:A	donor_loss	1.0000
20:62122793:GGTAG:G	donor_loss	1.0000
20:62124613:T:G	acceptor_gain	1.0000
20:62124614:A:AG	acceptor_gain	1.0000
20:62124614:AAGT:A	acceptor_gain	1.0000
20:62124615:A:G	acceptor_gain	1.0000
20:62124616:GT:G	acceptor_gain	1.0000
20:62124616:GTGA:G	acceptor_gain	1.0000
20:62124777:TCAGG:T	donor_loss	1.0000
20:62124778:CAGGT:C	donor_loss	1.0000
20:62124779:AGG:A	donor_loss	1.0000
20:62124780:GGT:G	donor_loss	1.0000
20:62124781:G:C	donor_loss	1.0000
20:62124781:G:GG	donor_gain	1.0000
20:62129950:GCG:G	donor_gain	1.0000
20:62129953:G:GG	donor_gain	1.0000
20:62131351:T:TA	acceptor_gain	1.0000
20:62131354:A:AG	acceptor_gain	1.0000
20:62131354:AGAT:A	acceptor_gain	1.0000
20:62131355:G:GA	acceptor_gain	1.0000
20:62131355:GA:G	acceptor_gain	1.0000
20:62131355:GAT:G	acceptor_gain	1.0000
20:62131355:GATG:G	acceptor_gain	1.0000
20:62131355:GATGA:G	acceptor_gain	1.0000
20:62131504:CAGGT:C	donor_loss	1.0000
20:62131506:GGTG:G	donor_loss	1.0000
20:62131507:G:GA	donor_loss	1.0000

AlphaMissense

2512 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:62122697:G:C	G11R	1.000
20:62122698:G:A	G11D	1.000
20:62122698:G:T	G11V	1.000
20:62122707:T:A	I14N	1.000
20:62122707:T:C	I14T	1.000
20:62122707:T:G	I14S	1.000
20:62122713:T:A	L16H	1.000
20:62122713:T:C	L16P	1.000
20:62122713:T:G	L16R	1.000
20:62122718:T:C	S18P	1.000
20:62122719:C:A	S18Y	1.000
20:62122719:C:T	S18F	1.000
20:62122724:G:C	A20P	1.000
20:62122733:C:A	R23S	1.000
20:62122733:C:G	R23G	1.000
20:62122733:C:T	R23C	1.000
20:62122734:G:A	R23H	1.000
20:62122734:G:C	R23P	1.000
20:62122736:T:A	Y24N	1.000
20:62122736:T:C	Y24H	1.000
20:62122736:T:G	Y24D	1.000
20:62122737:A:C	Y24S	1.000
20:62122737:A:G	Y24C	1.000
20:62122742:G:A	G26S	1.000
20:62122742:G:C	G26R	1.000
20:62122742:G:T	G26C	1.000
20:62122743:G:A	G26D	1.000
20:62122743:G:C	G26A	1.000
20:62122743:G:T	G26V	1.000
20:62122748:C:T	L28F	1.000

dbSNP variants (sampled 300 via entrez): RS1000089661 (20:62123089 GC>G), RS1000372247 (20:62120873 C>T), RS1000460761 (20:62134694 C>T), RS1000561775 (20:62130967 C>T), RS1000635150 (20:62131261 G>C), RS1000689037 (20:62122151 C>T), RS1000702819 (20:62127775 A>G), RS1000765343 (20:62135587 T>C), RS1001108469 (20:62125273 G>C), RS1001146817 (20:62122050 G>A), RS1001197566 (20:62135794 A>T), RS1001477858 (20:62125018 C>T), RS1001590950 (20:62133983 C>T), RS1001620457 (20:62134199 T>A), RS1001762031 (20:62131340 C>T)

Disease associations

OMIM: gene MIM:620689 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST008403_15	Arterial stiffness index	7.000000e-06
GCST90011900_12	Serum alkaline phosphatase levels	2.000000e-09

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004517	arterial stiffness measurement
EFO:0004533	alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

33 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
trichostatin A	affects cotreatment, decreases expression	3
methylmercuric chloride	increases expression	2
Valproic Acid	affects expression, decreases expression	2
GSK-J4	increases expression	1
FR900359	affects phosphorylation	1
geldanamycin	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
arsenite	decreases reaction, affects binding	1
sodium arsenite	increases expression, increases abundance	1
coumarin	decreases phosphorylation	1
di-n-butylphosphoric acid	affects expression	1
2,3,5-(triglutathion-S-yl)hydroquinone	increases ADP-ribosylation	1
monomethylarsonous acid	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
torcetrapib	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
MT19c compound	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Vorinostat	decreases expression	1
Arsenic	increases abundance, increases expression	1
Benzo(a)pyrene	decreases expression	1
Caffeine	affects phosphorylation	1
Diethylhexyl Phthalate	increases expression	1
Ivermectin	decreases expression	1
Methotrexate	increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Ribonucleotides	affects binding	1
Rotenone	increases expression	1
Thimerosal	decreases expression	1

Clinical trials (associated diseases)

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