SDS

serine dehydratase

Basic information

Region (hg38): 12:113392444-113426301

Links

ENSG00000135094 ∙ NCBI:10993 ∙ OMIM:182128 ∙ HGNC:10691 ∙ Uniprot:P20132 ∙ 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 SDS gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SDS 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				3		3
missense			25	1	1	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	4	1

Variants in SDS

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

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

Position	Type	Phenotype	Significance	ClinVar
12-113392988-G-A		not specified	Uncertain significance (Aug 08, 2023)
12-113393092-C-G		not specified	Uncertain significance (Jan 06, 2023)
12-113393102-C-T		not specified	Uncertain significance (Jan 10, 2023)
12-113393140-T-C		not specified	Uncertain significance (Jul 13, 2021)
12-113397177-G-T		not specified	Uncertain significance (Jun 07, 2023)
12-113397282-C-T		not specified	Uncertain significance (May 24, 2023)
12-113397310-C-T		not specified	Uncertain significance (Apr 27, 2022)
12-113397314-G-A			Likely benign (Jun 06, 2018)
12-113397331-T-C		not specified	Uncertain significance (Dec 02, 2022)
12-113397383-G-T		not specified	Uncertain significance (Jul 22, 2022)
12-113398519-T-G		not specified	Uncertain significance (Jun 22, 2023)
12-113398536-G-T		not specified	Uncertain significance (Mar 02, 2023)
12-113398557-G-A		not specified	Uncertain significance (Mar 06, 2023)
12-113398569-G-A		not specified	Uncertain significance (May 05, 2023)
12-113398588-C-G		not specified	Uncertain significance (Jun 21, 2022)
12-113398594-C-T		not specified	Uncertain significance (Jan 08, 2024)
12-113398748-G-C		not specified	Uncertain significance (Nov 08, 2022)
12-113398751-C-T		not specified	Uncertain significance (Mar 06, 2023)
12-113398781-C-T		not specified	Uncertain significance (Aug 30, 2021)
12-113398799-C-T			Likely benign (Aug 09, 2018)
12-113398805-G-T		not specified	Uncertain significance (Aug 22, 2023)
12-113398839-G-A			Likely benign (Jul 27, 2018)
12-113399561-T-C		not specified	Uncertain significance (Oct 06, 2021)
12-113399624-G-A		not specified	Uncertain significance (Dec 20, 2021)
12-113399631-G-A			Likely benign (Jun 06, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SDS	protein_coding	protein_coding	ENST00000257549	7	33857

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000139	0.869	125711	0	35	125746	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	164	206	0.797	0.0000127	2100
Missense in Polyphen		57	69.491	0.82024		697
Synonymous	-0.0331	99	98.6	1.00	0.00000732	701
Loss of Function	1.38	8	13.5	0.594	6.57e-7	153

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000868	0.0000868
Ashkenazi Jewish	0.00	0.00
East Asian	0.000653	0.000653
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000983	0.0000967
Middle Eastern	0.000653	0.000653
South Asian	0.000198	0.000196
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Cysteine and methionine metabolism - Homo sapiens (human);Glycine, serine and threonine metabolism - Homo sapiens (human);Valine, leucine and isoleucine biosynthesis - Homo sapiens (human);3-Phosphoglycerate dehydrogenase deficiency;Non Ketotic Hyperglycinemia;Ammonia Recycling;Glycine and Serine Metabolism;Dimethylglycine Dehydrogenase Deficiency;Hyperglycinemia, non-ketotic;Dimethylglycine Dehydrogenase Deficiency;Sarcosinemia;Threonine and 2-Oxobutanoate Degradation;Dihydropyrimidine Dehydrogenase Deficiency (DHPD);Amino Acid metabolism;Pathways in clear cell renal cell carcinoma;Metabolism of amino acids and derivatives;Glycine Serine metabolism;Metabolism;threonine degradation;Threonine catabolism (Consensus)

Recessive Scores

• pRec: 0.388

Intolerance Scores

• loftool: 0.243
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.56

Haploinsufficiency Scores

• pHI: 0.235
• hipred: N
• hipred_score: 0.282
• ghis: 0.462

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.305

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sds

Gene ontology

• Biological process: gluconeogenesis;L-serine catabolic process;threonine catabolic process;L-threonine catabolic process to glycine;pyruvate biosynthetic process
• Cellular component: mitochondrion;cytosol
• Molecular function: L-serine ammonia-lyase activity;L-threonine ammonia-lyase activity;hydro-lyase activity;pyridoxal phosphate binding;protein homodimerization activity