LIN28A

lin-28 homolog A, the group of Zinc fingers CCHC-type

Basic information

Region (hg38): 1:26410816-26429728

Previous symbols: [ "LIN28" ]

Links

ENSG00000131914 ∙ NCBI:79727 ∙ OMIM:611043 ∙ HGNC:15986 ∙ Uniprot:Q9H9Z2 ∙ 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 LIN28A gene.

• Inborn genetic diseases (7 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIN28A 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	1

Variants in LIN28A

This is a list of pathogenic ClinVar variants found in the LIN28A region.

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

Position	Type	Phenotype	Significance	ClinVar
1-26411441-C-G			Benign (Mar 29, 2018)
1-26411454-G-A		not specified	Uncertain significance (May 01, 2022)
1-26425442-G-A		not specified	Uncertain significance (Sep 16, 2021)
1-26426250-A-G		not specified	Uncertain significance (Apr 13, 2022)
1-26426354-C-G		not specified	Uncertain significance (Jul 05, 2023)
1-26426372-C-G		not specified	Uncertain significance (Oct 26, 2021)
1-26426394-C-T		not specified	Uncertain significance (Jul 27, 2021)
1-26426403-G-A		not specified	Uncertain significance (Oct 05, 2023)
1-26426415-A-G		not specified	Uncertain significance (Oct 12, 2022)
1-26426433-C-T		not specified	Uncertain significance (Dec 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LIN28A	protein_coding	protein_coding	ENST00000326279	4	18945

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0194	0.908	125740	0	7	125747	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.714	104	127	0.821	0.00000650	1367
Missense in Polyphen		19	31.436	0.60441		376
Synonymous	0.148	49	50.3	0.973	0.00000251	401
Loss of Function	1.52	4	8.90	0.449	4.42e-7	106

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000869	0.0000869
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000271	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding protein that inhibits processing of pre-let- 7 miRNAs and regulates translation of mRNAs that control developmental timing, pluripotency and metabolism (PubMed:21247876). Seems to recognize a common structural G- quartet (G4) feature in its miRNA and mRNA targets (Probable). 'Translational enhancer' that drives specific mRNAs to polysomes and increases the efficiency of protein synthesis. Its association with the translational machinery and target mRNAs results in an increased number of initiation events per molecule of mRNA and, indirectly, in mRNA stabilization. Binds IGF2 mRNA, MYOD1 mRNA, ARBP/36B4 ribosomal protein mRNA and its own mRNA. Essential for skeletal muscle differentiation program through the translational up-regulation of IGF2 expression. Suppressor of microRNA (miRNA) biogenesis, including that of let-7, miR107, miR-143 and miR-200c. Specifically binds the miRNA precursors (pre-miRNAs), recognizing an 5'-GGAG-3' motif found in pre-miRNA terminal loop, and recruits TUT4 AND tut7 uridylyltransferaseS. This results in the terminal uridylation of target pre-miRNAs. Uridylated pre-miRNAs fail to be processed by Dicer and undergo degradation. The repression of let- 7 expression is required for normal development and contributes to maintain the pluripotent state by preventing let-7-mediated differentiation of embryonic stem cells (PubMed:18951094, PubMed:19703396, PubMed:22118463, PubMed:22898984). Localized to the periendoplasmic reticulum area, binds to a large number of spliced mRNAs and inhibits the translation of mRNAs destined for the ER, reducing the synthesis of transmembrane proteins, ER or Golgi lumen proteins, and secretory proteins. Binds to and enhances the translation of mRNAs for several metabolic enzymes, such as PFKP, PDHA1 or SDHA, increasing glycolysis and oxidative phosphorylation. Which, with the let-7 repression may enhance tissue repair in adult tissue (By similarity). {ECO:0000250|UniProtKB:Q8K3Y3, ECO:0000269|PubMed:18951094, ECO:0000269|PubMed:19703396, ECO:0000269|PubMed:21247876, ECO:0000269|PubMed:22118463, ECO:0000269|PubMed:22898984, ECO:0000305}.
• Pathway: Cardiac Progenitor Differentiation;Developmental Biology;Transcriptional regulation of pluripotent stem cells (Consensus)

Recessive Scores

• pRec: 0.133

Intolerance Scores

• rvis_EVS: -0.3
• rvis_percentile_EVS: 32.62

Haploinsufficiency Scores

• pHI: 0.923
• hipred: Y
• hipred_score: 0.550
• ghis: 0.469

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lin28a
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); normal 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); reproductive system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: lin28a
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: regulation of transcription, DNA-templated;germ cell development;miRNA catabolic process;negative regulation of translation;stem cell population maintenance;pre-miRNA processing;RNA 3'-end processing;positive regulation of TOR signaling;somatic stem cell population maintenance;positive regulation of neuron differentiation;negative regulation of glial cell differentiation;stem cell differentiation;positive regulation of protein kinase B signaling;cellular response to glucose stimulus;positive regulation of cell proliferation involved in kidney development;positive regulation of production of miRNAs involved in gene silencing by miRNA;positive regulation of cytoplasmic translation
• Cellular component: P-body;nucleus;nucleolus;cytoplasm;rough endoplasmic reticulum;cytosol;polysome;cytoplasmic stress granule;ribonucleoprotein complex
• Molecular function: G-quadruplex RNA binding;DNA binding;RNA binding;protein binding;zinc ion binding;translation initiation factor binding;miRNA binding;polysome binding;sequence-specific mRNA binding