LSM14A

protein-coding

LSM14A mRNA processing body assembly factor, the group of LSm proteins

Gene summary

Sm-like proteins were identified in a variety of organisms based on sequence homology with the Sm protein family (see SNRPD2; 601061). Sm-like proteins contain the Sm sequence motif, which consists of 2 regions separated by a linker of variable length that folds as a loop. The Sm-like proteins are thought to form a stable heteromer present in tri-snRNP particles, which are important for pre-mRNA splicing.[supplied by OMIM, Mar 2008]

Previous symbols:

C19orf13
FAM61A

MANE transcript

NM_015578.4

Inheritance

—

ClinVar variants

U:50B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.29

Max pathogenic AF

—

Genomic locus

chr19:34,172,504-34,229,288

External References & Databases

Ensembl (ENSG00000257103)

Transcript & Mutation Effects

hg38 • Region Span ~56.8 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 LSM14A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 44

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015578.4. 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				1 clinvar		1
missense			47 clinvar	1 clinvar		48
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	50	2	0	52

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 88 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015578.4	RefSeq	NP_056393.2	10	MANE Select
ENST00000544216.8	Ensembl	ENSP00000446271.2	10	MANE Select
NM_001114093.3	RefSeq	NP_001107565.1	10	Standard
NM_001384420.1	RefSeq	NP_001371349.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of translation
multicellular organism development
cytoplasmic mRNA processing body assembly
RIG-I signaling pathway
positive regulation of type I interferon-mediated signaling pathway

Molecular Function

double-stranded DNA binding
RNA binding
double-stranded RNA binding
single-stranded RNA binding

Cellular Component

P-body
cytoplasm
cytosol
cytoplasmic stress granule
cytoplasmic ribonucleoprotein granule

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000544216
Coding exons: 10
Length: 57012
Individuals with no LoFs: 125730
Homozygous LoFs: 0
Heterozygous LoFs: 16
Defined: 125746
p: 0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.91	180	268	0.671	0.0000149	2998
Missense (PolyPhen)		34	71.879	0.47302		862
Synonymous	1.25	75	90.1	0.833	0.00000458	922
Loss of Function	3.20	7	23.9	0.293	0.00000137	277

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000036	0.000035	rare
South Asian	0.000033	0.000033	rare
Other	0.00018	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Essential for formation of P-bodies, cytoplasmic structures that provide storage sites for non-translating mRNAs. {ECO:0000269|PubMed:16484376, ECO:0000269|PubMed:17074753}.;

Recessive Scores

pRec: 0.120

Intolerance Scores

LoFtool: 0.705
RVIS EVS: 0.26
RVIS percentile EVS: 70.26

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.149

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium