LYAR

Ly1 antibody reactive, the group of Zinc fingers C2HC-type

Basic information

Region (hg38): 4:4267701-4290154

Links

ENSG00000145220 ∙ NCBI:55646 ∙ OMIM:617684 ∙ HGNC:26021 ∙ Uniprot:Q9NX58 ∙ 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 LYAR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LYAR 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						0
missense			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	0

Variants in LYAR

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

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

Position	Type	Phenotype	Significance	ClinVar
4-4267926-A-C		not specified	Uncertain significance (Jun 02, 2023)
4-4267932-G-C		not specified	Uncertain significance (Sep 26, 2023)
4-4267938-T-C		not specified	Uncertain significance (Aug 08, 2023)
4-4273595-C-G		not specified	Uncertain significance (Jun 28, 2022)
4-4273601-C-T		not specified	Uncertain significance (Jul 13, 2021)
4-4274372-G-A		not specified	Uncertain significance (Feb 03, 2022)
4-4274442-T-G		not specified	Uncertain significance (Jan 04, 2024)
4-4274474-T-A		not specified	Uncertain significance (May 17, 2023)
4-4274580-T-G		not specified	Uncertain significance (May 13, 2024)
4-4274590-C-A		not specified	Uncertain significance (Aug 13, 2021)
4-4274636-T-A		not specified	Uncertain significance (Jul 05, 2023)
4-4274649-C-A		not specified	Uncertain significance (Dec 21, 2023)
4-4274742-G-A		not specified	Uncertain significance (Nov 21, 2022)
4-4274763-C-T		not specified	Uncertain significance (Aug 12, 2021)
4-4279481-T-C		not specified	Uncertain significance (Sep 23, 2023)
4-4279491-T-A		not specified	Uncertain significance (Jun 22, 2024)
4-4279506-C-G		not specified	Uncertain significance (Feb 16, 2023)
4-4279669-G-T		not specified	Uncertain significance (Nov 21, 2023)
4-4279690-C-G		not specified	Uncertain significance (Jan 05, 2022)
4-4279722-T-A		not specified	Uncertain significance (Apr 04, 2023)
4-4281812-C-G		not specified	Uncertain significance (May 27, 2022)
4-4281813-T-A		not specified	Uncertain significance (Mar 21, 2023)
4-4281847-T-A		not specified	Uncertain significance (May 23, 2023)
4-4281886-T-C		not specified	Uncertain significance (May 29, 2024)
4-4283681-T-C		not specified	Uncertain significance (Jul 20, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LYAR	protein_coding	protein_coding	ENST00000343470	8	22469

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.76e-7	0.815	125713	0	34	125747	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.218	211	202	1.04	0.0000106	2536
Missense in Polyphen		42	41.065	1.0228		576
Synonymous	-1.33	89	74.4	1.20	0.00000440	631
Loss of Function	1.43	13	19.9	0.654	9.34e-7	260

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000184	0.000184
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.000212	0.000211
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000493	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the maintenance of the appropriate processing of 47S/45S pre-rRNA to 32S/30S pre-rRNAs and their subsequent processing to produce 18S and 28S rRNAs (PubMed:24495227). Also acts at the level of transcription regulation. Along with PRMT5, binds the gamma-globin (HBG1/HBG2) promoter and represses its expression (PubMed:25092918). In neuroblastoma cells, may also repress the expression of oxidative stress genes, including CHAC1, HMOX1, SLC7A11, ULBP1 and SNORD41 that encodes a small nucleolar RNA (PubMed:28686580). Preferentially binds to a DNA motif containing 5'-GGTTAT-3' (PubMed:25092918). Stimulates phagocytosis of photoreceptor outer segments by retinal pigment epithelial cells (By similarity). Prevents nucleolin/NCL self-cleavage, maintaining a normal steady- state level of NCL protein in undifferentiated embryonic stem cells (ESCs), which in turn is essential for ESC self-renewal (By similarity). {ECO:0000250|UniProtKB:Q08288, ECO:0000269|PubMed:24495227, ECO:0000269|PubMed:25092918, ECO:0000269|PubMed:28686580}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.54

Haploinsufficiency Scores

• pHI: 0.706
• hipred: Y
• hipred_score: 0.658
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.393

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lyar
• Phenotype: embryo phenotype; neoplasm; 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); limbs/digits/tail 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); cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;rRNA processing;erythrocyte development;positive regulation of phagocytosis
• Cellular component: photoreceptor outer segment;nucleus;nucleolus;cytoplasm
• Molecular function: DNA binding;RNA binding;protein binding;metal ion binding