LSM14A

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

Basic information

Region (hg38): 19:34172504-34229288

Previous symbols: [ "C19orf13", "FAM61A" ]

Links

ENSG00000257103 ∙ NCBI:26065 ∙ OMIM:610677 ∙ HGNC:24489 ∙ Uniprot:Q8ND56 ∙ 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 LSM14A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LSM14A 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		1
missense			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in LSM14A

This is a list of pathogenic ClinVar variants found in the LSM14A region.

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

Position	Type	Phenotype	Significance	ClinVar
19-34172672-C-T			Likely benign (Dec 01, 2022)
19-34196671-T-A		not specified	Uncertain significance (Apr 28, 2022)
19-34208995-C-G		not specified	Uncertain significance (Nov 17, 2023)
19-34209019-A-G		not specified	Uncertain significance (Oct 20, 2023)
19-34215168-A-G		not specified	Uncertain significance (Sep 26, 2023)
19-34215189-G-A		not specified	Uncertain significance (Dec 20, 2023)
19-34215644-A-G		not specified	Uncertain significance (Dec 20, 2023)
19-34219756-G-C		not specified	Uncertain significance (Oct 16, 2023)
19-34219789-A-C		not specified	Uncertain significance (Aug 16, 2021)
19-34219795-G-A		not specified	Uncertain significance (Jul 14, 2021)
19-34221512-G-A		not specified	Uncertain significance (Oct 13, 2023)
19-34221565-C-T		not specified	Uncertain significance (Dec 30, 2023)
19-34221637-C-T		not specified	Uncertain significance (Mar 20, 2023)
19-34221674-G-A		not specified	Uncertain significance (Jan 02, 2024)
19-34221682-C-A		not specified	Uncertain significance (May 11, 2022)
19-34221704-G-A		not specified	Uncertain significance (Feb 15, 2023)
19-34221737-G-C		not specified	Uncertain significance (Nov 27, 2023)
19-34226415-C-T		not specified	Uncertain significance (Feb 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LSM14A	protein_coding	protein_coding	ENST00000544216	10	57012

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0399	0.960	125730	0	16	125746	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.91	180	268	0.671	0.0000149	2998
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000307	0.000306
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.0000548	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000356	0.0000352
Middle Eastern	0.0000548	0.0000544
South Asian	0.0000328	0.0000327
Other	0.000181	0.000163

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.869
• hipred: Y
• hipred_score: 0.625
• ghis: 0.590

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.149

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lsm14a
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• 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
• Cellular component: P-body;cytoplasm;cytosol;cytoplasmic stress granule;cytoplasmic ribonucleoprotein granule
• Molecular function: double-stranded DNA binding;RNA binding;double-stranded RNA binding;single-stranded RNA binding