SCLY

selenocysteine lyase

Basic information

Region (hg38): 2:238060924-238099413

Links

ENSG00000132330 ∙ NCBI:51540 ∙ OMIM:611056 ∙ HGNC:18161 ∙ Uniprot:Q96I15 ∙ 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 SCLY gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCLY 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	2	3
missense			55	4	3	62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			1			1
Total	0	0	56	5	5

Variants in SCLY

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

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

Position	Type	Phenotype	Significance	ClinVar
2-238061049-G-T		not specified	Uncertain significance (Aug 17, 2022)
2-238061086-C-T		not specified	Uncertain significance (Jul 14, 2022)
2-238061088-C-G		not specified	Uncertain significance (Feb 12, 2024)
2-238061089-C-G		not specified	Likely benign (Jan 18, 2025)
2-238061101-C-G		not specified	Uncertain significance (Jan 08, 2025)
2-238064382-A-G		not specified	Uncertain significance (Feb 28, 2025)
2-238064417-G-T		not specified	Uncertain significance (Jan 23, 2024)
2-238064458-C-T		not specified	Likely benign (Dec 22, 2023)
2-238068068-G-T		not specified	Uncertain significance (Jul 26, 2024)
2-238068073-G-A		not specified	Uncertain significance (Aug 04, 2022)
2-238068080-A-G		not specified	Uncertain significance (Feb 27, 2024)
2-238068097-C-T		not specified	Uncertain significance (Sep 12, 2023)
2-238068120-A-G			Benign (Mar 02, 2018)
2-238068122-G-T		not specified	Uncertain significance (May 31, 2023)
2-238068129-A-T		not specified	Uncertain significance (Mar 05, 2025)
2-238068152-C-T		not specified	Uncertain significance (Oct 29, 2024)
2-238068154-G-A		not specified	Uncertain significance (Sep 29, 2023)
2-238068161-C-G		not specified	Uncertain significance (Dec 13, 2023)
2-238068161-C-T		not specified	Uncertain significance (Sep 02, 2024)
2-238069423-G-C		not specified	Uncertain significance (Aug 12, 2021)
2-238069439-G-A		not specified	Uncertain significance (Jan 30, 2025)
2-238081723-C-G		not specified	Uncertain significance (Jun 29, 2023)
2-238081724-C-T		not specified	Uncertain significance (Feb 27, 2023)
2-238081759-G-A		not specified	Uncertain significance (Jan 26, 2023)
2-238081777-C-T		not specified	Uncertain significance (May 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCLY	protein_coding	protein_coding	ENST00000254663	12	38525

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.33e-9	0.454	125676	0	72	125748	0.000286

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0912	289	285	1.02	0.0000185	2932
Missense in Polyphen		107	107.3	0.99717		1046
Synonymous	1.01	104	118	0.881	0.00000844	919
Loss of Function	1.02	16	21.1	0.759	0.00000107	242

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000513	0.000511
Ashkenazi Jewish	0.00	0.00
East Asian	0.000165	0.000163
Finnish	0.000419	0.000416
European (Non-Finnish)	0.000195	0.000193
Middle Eastern	0.000165	0.000163
South Asian	0.000838	0.000817
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the decomposition of L-selenocysteine to L- alanine and elemental selenium. {ECO:0000250}.
• Pathway: Selenocompound metabolism - Homo sapiens (human);Selenoamino Acid Metabolism;Selenium Metabolism and Selenoproteins;Metabolism of amino acids and derivatives;Metabolism;Selenoamino acid metabolism;Metabolism of ingested SeMet, Sec, MeSec into H2Se (Consensus)

Recessive Scores

• pRec: 0.166

Intolerance Scores

• loftool: 0.268
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.49

Haploinsufficiency Scores

• pHI: 0.394
• hipred: N
• hipred_score: 0.251
• ghis: 0.401

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.885

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scly
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: selenium compound metabolic process;cellular amino acid metabolic process
• Cellular component: cytosol
• Molecular function: protein binding;selenocysteine lyase activity;transferase activity