SRR

serine racemase

Basic information

Region (hg38): 17:2303383-2325260

Links

ENSG00000167720 ∙ NCBI:63826 ∙ OMIM:606477 ∙ HGNC:14398 ∙ Uniprot:Q9GZT4 ∙ 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 SRR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SRR 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						0
missense			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			13	1		14
Total	0	0	28	2	0

Variants in SRR

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

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

Position	Type	Phenotype	Significance	ClinVar
17-2303657-G-C		not specified	Uncertain significance (Sep 15, 2021)
17-2303674-C-T		not specified	Uncertain significance (Aug 04, 2023)
17-2303711-C-T		not specified	Uncertain significance (May 09, 2024)
17-2315669-C-G		not specified	Likely benign (Jan 24, 2023)
17-2315705-T-C		not specified	Uncertain significance (Oct 25, 2022)
17-2317874-G-A		not specified	Uncertain significance (Sep 29, 2023)
17-2317874-G-C		not specified	Uncertain significance (Aug 12, 2021)
17-2318883-T-C		not specified	Uncertain significance (Dec 06, 2023)
17-2321405-G-A		not specified	Uncertain significance (Mar 07, 2024)
17-2321542-G-T		not specified	Uncertain significance (Sep 10, 2024)
17-2321597-G-C		not specified	Uncertain significance (Oct 30, 2023)
17-2321600-T-C		not specified	Uncertain significance (May 16, 2022)
17-2323161-A-G		not specified	Uncertain significance (Oct 27, 2023)
17-2323211-G-A		not specified	Uncertain significance (Jan 18, 2023)
17-2323275-G-A		not specified	Uncertain significance (Jan 19, 2022)
17-2323314-A-G		not specified	Uncertain significance (Nov 13, 2024)
17-2323317-T-A		not specified	Uncertain significance (May 08, 2024)
17-2323736-C-G		not specified	Uncertain significance (Dec 15, 2022)
17-2323738-A-C		not specified	Uncertain significance (Aug 04, 2023)
17-2323748-A-G		not specified	Uncertain significance (Sep 25, 2024)
17-2323751-G-A		not specified	Uncertain significance (Nov 07, 2022)
17-2323758-C-T		not specified	Uncertain significance (Sep 25, 2024)
17-2323860-C-T		not specified	Uncertain significance (Feb 15, 2023)
17-2324231-T-C		not specified	Uncertain significance (Dec 19, 2023)
17-2324249-G-A		not specified	Uncertain significance (Feb 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SRR	protein_coding	protein_coding	ENST00000344595	7	21878

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00580	0.974	125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.881	148	181	0.816	0.00000849	2206
Missense in Polyphen		53	56.7	0.93474		718
Synonymous	0.0312	64	64.3	0.995	0.00000311	705
Loss of Function	2.03	6	14.3	0.419	6.70e-7	177

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000529	0.000529
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.000185	0.000185
European (Non-Finnish)	0.0000971	0.0000967
Middle Eastern	0.000217	0.000217
South Asian	0.000196	0.000196
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the synthesis of D-serine from L-serine. D- serine is a key coagonist with glutamate at NMDA receptors. Has dehydratase activity towards both L-serine and D-serine. {ECO:0000269|PubMed:11054547, ECO:0000269|PubMed:20106978}.
• Pathway: Glycine, serine and threonine metabolism - Homo sapiens (human);3-Phosphoglycerate dehydrogenase deficiency;Non Ketotic Hyperglycinemia;Glycine and Serine Metabolism;Dimethylglycine Dehydrogenase Deficiency;Hyperglycinemia, non-ketotic;Dimethylglycine Dehydrogenase Deficiency;Sarcosinemia;Dihydropyrimidine Dehydrogenase Deficiency (DHPD);Metabolism of amino acids and derivatives;Metabolism;serine and glycine biosynthesis;Amino acid synthesis and interconversion (transamination);Serine biosynthesis (Consensus)

Recessive Scores

• pRec: 0.220

Intolerance Scores

• loftool: 0.452
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.04

Haploinsufficiency Scores

• pHI: 0.506
• hipred: N
• hipred_score: 0.293
• ghis: 0.615

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.683

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Srr
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: L-serine metabolic process;L-serine biosynthetic process;brain development;aging;serine family amino acid metabolic process;response to lipopolysaccharide;pyruvate biosynthetic process;response to morphine;protein homotetramerization;D-serine metabolic process;D-serine biosynthetic process
• Cellular component: cytoplasm;cytosol;plasma membrane;neuronal cell body;apical part of cell
• Molecular function: magnesium ion binding;L-serine ammonia-lyase activity;calcium ion binding;ATP binding;D-serine ammonia-lyase activity;glycine binding;threonine racemase activity;PDZ domain binding;pyridoxal phosphate binding;serine racemase activity;protein homodimerization activity