SCLY

protein-coding

selenocysteine lyase

Gene summary

Selenocysteine lyase (SCLY; EC 4.4.1.16) catalyzes the pyridoxal 5-prime phosphate-dependent conversion of L-selenocysteine to L-alanine and elemental selenium (Mihara et al., 2000 [PubMed 10692412]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_016510.7

Inheritance

—

ClinVar variants

U:96B:13

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.76

Max pathogenic AF

—

Genomic locus

chr2:238,060,924-238,099,413

External References & Databases

Ensembl (ENSG00000132330)

Transcript & Mutation Effects

hg38 • Region Span ~38.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SCLY variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 103

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016510.7. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	2 clinvar	3
missense			96 clinvar	7 clinvar	3 clinvar	106
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	96	8	5	109

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016510.7	RefSeq	NP_057594.5	12	MANE Select
ENST00000254663.12	Ensembl	ENSP00000254663.7	12	MANE Select
ENST00000409736.6	Ensembl	ENSP00000387162.2	8	Standard
ENST00000409736.7	Ensembl	ENSP00000387162.2	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Selenocompound metabolism - Homo sapiens (human)
Selenoamino Acid Metabolism
Selenium Metabolism and Selenoproteins
Metabolism of amino acids and derivatives
Metabolism

Biological Process

selenium compound metabolic process
cellular amino acid metabolic process

Molecular Function

protein binding
selenocysteine lyase activity
transferase activity

Cellular Component

cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000254663
Coding exons: 12
Length: 38525
Individuals with no LoFs: 125676
Homozygous LoFs: 0
Heterozygous LoFs: 72
Defined: 125748
p: 0.000286

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0912	289	285	1.02	0.0000185	2932
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.00042	0.00042	rare
European (Non-Finnish)	0.00020	0.00019	rare
South Asian	0.00084	0.00082	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Catalyzes the decomposition of L-selenocysteine to L- alanine and elemental selenium. {ECO:0000250}.;

Recessive Scores

pRec: 0.166

Intolerance Scores

LoFtool: 0.268
RVIS EVS: 0.22
RVIS percentile EVS: 68.49

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.885

Gene Damage Prediction

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