LAYN

layilin, the group of C-type lectin domain containing

Basic information

Region (hg38): 11:111540280-111561745

Links

ENSG00000204381 ∙ NCBI:143903 ∙ OMIM:618843 ∙ HGNC:29471 ∙ Uniprot:Q6UX15 ∙ 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 LAYN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LAYN 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			22	1	3	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	22	1	4

Variants in LAYN

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

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

Position	Type	Phenotype	Significance	ClinVar
11-111540860-C-T		not specified	Uncertain significance (May 26, 2024)
11-111540878-T-G		not specified	Uncertain significance (Apr 25, 2022)
11-111540883-G-A			Benign (Apr 19, 2018)
11-111540902-G-A		not specified	Uncertain significance (Sep 22, 2023)
11-111540917-G-T		not specified	Uncertain significance (May 07, 2024)
11-111541559-C-T			Benign (Jun 16, 2021)
11-111543953-G-A		not specified	Uncertain significance (May 21, 2024)
11-111543967-G-A		not specified	Uncertain significance (May 05, 2023)
11-111544004-T-G		not specified	Uncertain significance (Apr 25, 2022)
11-111544009-G-A			Benign (Dec 31, 2019)
11-111544060-T-G		not specified	Uncertain significance (Apr 17, 2024)
11-111544144-C-T		not specified	Uncertain significance (Jan 23, 2024)
11-111544145-G-A		not specified	Uncertain significance (Aug 12, 2021)
11-111544196-C-G		not specified	Uncertain significance (Apr 04, 2024)
11-111549667-A-T		not specified	Uncertain significance (Jun 07, 2023)
11-111549697-A-G		not specified	Uncertain significance (Feb 26, 2024)
11-111549707-C-T		not specified	Uncertain significance (May 23, 2023)
11-111549734-G-A		not specified	Uncertain significance (Feb 28, 2023)
11-111555225-C-A		not specified	Uncertain significance (May 03, 2023)
11-111555263-G-A		not specified	Uncertain significance (Nov 08, 2022)
11-111555285-G-A		not specified	Likely benign (May 02, 2024)
11-111557603-G-A		not specified	Uncertain significance (Aug 04, 2021)
11-111560099-C-T		not specified	Uncertain significance (May 27, 2022)
11-111560114-C-T		not specified	Uncertain significance (Apr 07, 2022)
11-111560136-C-G		not specified	Uncertain significance (Dec 07, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LAYN	protein_coding	protein_coding	ENST00000375615	8	21260

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.34e-13	0.0252	125680	0	68	125748	0.000270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.372	198	213	0.928	0.0000110	2496
Missense in Polyphen		54	71.881	0.75124		856
Synonymous	0.718	73	81.2	0.899	0.00000436	724
Loss of Function	0.0688	20	20.3	0.984	0.00000102	224

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000933	0.000933
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000163
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000203	0.000202
Middle Eastern	0.000167	0.000163
South Asian	0.000264	0.000261
Other	0.000344	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for hyaluronate. {ECO:0000269|PubMed:11294894}.

Recessive Scores

• pRec: 0.0959

Intolerance Scores

• loftool: 0.886
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.51

Haploinsufficiency Scores

• pHI: 0.100
• hipred: N
• hipred_score: 0.251
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0997

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Layn

Gene ontology

• Cellular component: ruffle;focal adhesion;cell surface;integral component of membrane
• Molecular function: hyaluronic acid binding;carbohydrate binding