SDSL

serine dehydratase like

Basic information

Region (hg38): 12:113422380-113438276

Links

ENSG00000139410 ∙ NCBI:113675 ∙ ∙ HGNC:30404 ∙ Uniprot:Q96GA7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 35.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_001304993.2	NP_001291922.1	7	yes	-
ENST00000403593.9	ENSP00000385790.4	7	yes	-
NM_138432.4	NP_612441.1	7	-	-
ENST00000345635.8	ENSP00000341117.4	7	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• not_specified (57 variants)
• not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SDSL gene is commonly pathogenic or not. These statistics are base on transcript: NM_001304993.2. 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			1	1		2
missense			59	1		60
nonsense			2			2
start loss						0
frameshift				1		1
splice donor/acceptor (+/-2bp)			2			2
Total	0	0	64	3	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SDSL	protein_coding	protein_coding	ENST00000403593	7	16040

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		123749	9	1989	125747	0.00798

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0746	194	191	1.02	0.0000105	2093
Missense in Polyphen		69	63.027	1.0948		677
Synonymous	-0.119	87	85.6	1.02	0.00000536	714
Loss of Function	-0.767	15	12.1	1.24	5.15e-7	145

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0115	0.0113
Ashkenazi Jewish	0.0313	0.0308
East Asian	0.00506	0.00507
Finnish	0.00211	0.00199
European (Non-Finnish)	0.00989	0.00977
Middle Eastern	0.00506	0.00507
South Asian	0.00235	0.00232
Other	0.0125	0.0123

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has low serine dehydratase and threonine dehydratase activity.
• Pathway: Cysteine and methionine metabolism - Homo sapiens (human);Glycine, serine and threonine metabolism - Homo sapiens (human);Valine, leucine and isoleucine biosynthesis - Homo sapiens (human);Pathways in clear cell renal cell carcinoma;Metabolism of amino acids and derivatives;Metabolism;L-serine degradation;threonine degradation;Threonine catabolism (Consensus)

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.256
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.42

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.682

Gene Damage Prediction

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

Gene ontology

• Biological process: L-serine catabolic process;threonine catabolic process;biological_process;L-threonine catabolic process to glycine
• Cellular component: cytosol
• Molecular function: molecular_function;L-serine ammonia-lyase activity;L-threonine ammonia-lyase activity;hydro-lyase activity;pyridoxal phosphate binding;identical protein binding