LYSET

lysosomal enzyme trafficking factor

Basic information

Region (hg38): 14:93184951-93188463

Previous symbols: [ "C14orf109", "TMEM251" ]

Links

ENSG00000153485 ∙ NCBI:26175 ∙ OMIM:619332 ∙ HGNC:20218 ∙ Uniprot:Q8N6I4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• dysostosis multiplex, Ain-Naz type (Limited), mode of inheritance: AR
• dysostosis multiplex, Ain-Naz type (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Dysostosis multiplex, Ain-Naz type	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal	33252156

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LYSET gene.

• not_specified (21 variants)
• Dysostosis_multiplex,_Ain-Naz_type (2 variants)
• LYSET-related_disorder (1 variants)
• Intellectual_disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LYSET gene is commonly pathogenic or not. These statistics are base on transcript: NM_001098621.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense	1		20	2		23
nonsense		1				1
start loss						0
frameshift		2				2
splice donor/acceptor (+/-2bp)						0
Total	1	3	20	2	0

Highest pathogenic variant AF is 0.00000273687

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LYSET	protein_coding	protein_coding	ENST00000415050	2	2139

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00694	0.776	124776	0	19	124795	0.0000761

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.940	66	91.3	0.723	0.00000449	1093
Missense in Polyphen		31	39.59	0.78302		470
Synonymous	1.06	25	32.7	0.764	0.00000151	326
Loss of Function	0.931	4	6.58	0.608	2.76e-7	89

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.0000556	0.0000556
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.57
• rvis_percentile_EVS: 81.89

Haploinsufficiency Scores

• pHI: 0.190
• hipred: N
• hipred_score: 0.187

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem251

Gene ontology

• Cellular component: integral component of membrane