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GeneBe

SDS

serine dehydratase

Basic information

Region (hg38): 12:113392444-113426301

Links

ENSG00000135094NCBI:10993OMIM:182128HGNC:10691Uniprot:P20132AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

  • Inborn genetic diseases (23 variants)
  • not provided (5 variants)

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
clinvar
3
missense
23
clinvar
1
clinvar
1
clinvar
25
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 23 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)2617514
12-113393092-C-G not specified Uncertain significance (Jan 06, 2023)2474284
12-113393102-C-T not specified Uncertain significance (Jan 10, 2023)2474976
12-113393140-T-C not specified Uncertain significance (Jul 13, 2021)2236811
12-113397177-G-T not specified Uncertain significance (Jun 07, 2023)2525176
12-113397282-C-T not specified Uncertain significance (May 24, 2023)2551448
12-113397310-C-T not specified Uncertain significance (Apr 27, 2022)2357980
12-113397314-G-A Likely benign (Jun 06, 2018)745995
12-113397331-T-C not specified Uncertain significance (Dec 02, 2022)2332082
12-113397383-G-T not specified Uncertain significance (Jul 22, 2022)2303007
12-113398519-T-G not specified Uncertain significance (Jun 22, 2023)2605274
12-113398536-G-T not specified Uncertain significance (Mar 02, 2023)2471219
12-113398557-G-A not specified Uncertain significance (Mar 06, 2023)2463506
12-113398569-G-A not specified Uncertain significance (May 05, 2023)2562226
12-113398588-C-G not specified Uncertain significance (Jun 21, 2022)2379760
12-113398594-C-T not specified Uncertain significance (Jan 08, 2024)3159079
12-113398748-G-C not specified Uncertain significance (Nov 08, 2022)2324094
12-113398751-C-T not specified Uncertain significance (Mar 06, 2023)2494682
12-113398781-C-T not specified Uncertain significance (Aug 30, 2021)2247593
12-113398799-C-T Likely benign (Aug 09, 2018)708699
12-113398805-G-T not specified Uncertain significance (Aug 22, 2023)2621504
12-113398839-G-A Likely benign (Jul 27, 2018)726251
12-113399561-T-C not specified Uncertain significance (Oct 06, 2021)2308988
12-113399624-G-A not specified Uncertain significance (Dec 20, 2021)2403361
12-113399631-G-A Likely benign (Jun 06, 2018)745996

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SDSprotein_codingprotein_codingENST00000257549 733857
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0001390.8691257110351257460.000139
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.041642060.7970.00001272100
Missense in Polyphen5769.4910.82024697
Synonymous-0.03319998.61.000.00000732701
Loss of Function1.38813.50.5946.57e-7153

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00008680.0000868
Ashkenazi Jewish0.000.00
East Asian0.0006530.000653
Finnish0.00009240.0000924
European (Non-Finnish)0.00009830.0000967
Middle Eastern0.0006530.000653
South Asian0.0001980.000196
Other0.0001630.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sds
Phenotype

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