SDS

protein-coding

serine dehydratase

Gene summary

This gene encodes one of three enzymes that are involved in metabolizing serine and glycine. L-serine dehydratase converts L-serine to pyruvate and ammonia and requires pyridoxal phosphate as a cofactor. The encoded protein can also metabolize threonine to NH4+ and 2-ketobutyrate. The encoded protein is found predominantly in the liver. [provided by RefSeq, Jul 2008]

MANE transcript

NM_006843.3

Inheritance

—

ClinVar variants

U:62B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.59

Max pathogenic AF

—

Genomic locus

chr12:113,392,445-113,426,301

External References & Databases

Ensembl (ENSG00000135094)

Transcript & Mutation Effects

hg38 • Region Span ~33.9 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 SDS variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 60

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006843.3. 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	3 clinvar		4
missense			58 clinvar	2 clinvar	1 clinvar	61
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	62	5	1	68

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 54 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006843.3	RefSeq	NP_006834.2	7	MANE Select
ENST00000257549.9	Ensembl	ENSP00000257549.4	7	MANE Select
ENST00000547342.1	Ensembl	ENSP00000449061.1	6	Standard
ENST00000552280.5	Ensembl	ENSP00000449833.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

gluconeogenesis
L-serine catabolic process
threonine catabolic process
L-threonine catabolic process to glycine
pyruvate biosynthetic process

Molecular Function

L-serine ammonia-lyase activity
L-threonine ammonia-lyase activity
hydro-lyase activity
pyridoxal phosphate binding
protein homodimerization activity

Cellular Component

mitochondrion
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000257549
Coding exons: 7
Length: 33857
Individuals with no LoFs: 125711
Homozygous LoFs: 0
Heterozygous LoFs: 35
Defined: 125746
p: 0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.04	164	206	0.797	0.0000127	2100
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00065	0.00065	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.000098	0.000097	rare
South Asian	0.00020	0.00020	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.388

Intolerance Scores

LoFtool: 0.243
RVIS EVS: -0.42
RVIS percentile EVS: 25.56

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.305

Gene Damage Prediction

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