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GeneBe

SARDH

sarcosine dehydrogenase

Basic information

Region (hg38): 9:133663559-133739955

Previous symbols: [ "DMGDHL1" ]

Links

ENSG00000123453NCBI:1757OMIM:604455HGNC:10536Uniprot:Q9UL12AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • sarcosinemia (Supportive), mode of inheritance: AR
  • sarcosinemia (Limited), mode of inheritance: Unknown
  • sarcosinemia (Limited), mode of inheritance: AR

ClinVar

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

  • Inborn genetic diseases (44 variants)
  • not provided (26 variants)
  • Sarcosine dehydrogenase deficiency (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SARDH 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
4
clinvar
9
clinvar
13
missense
43
clinvar
7
clinvar
6
clinvar
56
nonsense
0
start loss
0
frameshift
1
clinvar
1
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
2
non coding
0
Total 0 1 43 11 15

Variants in SARDH

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

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

Position Type Phenotype Significance ClinVar
9-133663914-T-C not specified Uncertain significance (Dec 20, 2021)2268140
9-133663932-G-A not specified Uncertain significance (Sep 17, 2021)2251079
9-133664010-G-A not specified Uncertain significance (Dec 19, 2022)3157830
9-133666739-C-T not specified Uncertain significance (Aug 26, 2022)2398384
9-133666754-T-C not specified Likely benign (Dec 02, 2022)2332277
9-133666765-G-A Likely benign (Aug 01, 2022)2659696
9-133666768-G-A SARDH-related condition Likely benign (Apr 29, 2019)3055870
9-133666770-C-T not specified Uncertain significance (Mar 06, 2023)2461695
9-133666782-C-T not specified Likely benign (Jul 09, 2021)2363600
9-133666783-G-C not specified Uncertain significance (Jul 27, 2021)2383675
9-133666831-G-A SARDH-related condition Likely benign (Dec 24, 2019)3043833
9-133670611-C-T not specified Uncertain significance (Jan 07, 2022)2383414
9-133670612-G-A not specified Uncertain significance (Jun 22, 2023)2595790
9-133670615-G-A not specified Uncertain significance (Jul 13, 2021)2227018
9-133670624-C-T Benign (Dec 31, 2019)776458
9-133670630-G-A not specified Uncertain significance (Jul 20, 2021)2223514
9-133670635-T-C not specified Uncertain significance (Aug 23, 2021)2348133
9-133670733-C-T Benign (Feb 01, 2024)791575
9-133670734-G-A Likely benign (Jul 01, 2023)718828
9-133670747-G-A not specified Uncertain significance (Nov 13, 2023)3157829
9-133671557-G-A SARDH-related condition Benign (Oct 17, 2019)3059243
9-133671564-C-T not specified Uncertain significance (Aug 08, 2022)2406872
9-133671601-C-T not specified Uncertain significance (Mar 05, 2024)3157828
9-133671628-C-G not specified Likely benign (Dec 27, 2023)3157827
9-133671635-C-T Likely benign (May 01, 2022)729020

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SARDHprotein_codingprotein_codingENST00000371872 2076396
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
5.27e-160.91712545502931257480.00117
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.6795616080.9230.00004075870
Missense in Polyphen194245.770.789362404
Synonymous0.1022622640.9920.00001921872
Loss of Function2.233248.80.6550.00000285471

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.002030.00195
Ashkenazi Jewish0.001900.00189
East Asian0.0005020.000489
Finnish0.003340.00329
European (Non-Finnish)0.001120.00111
Middle Eastern0.0005020.000489
South Asian0.0004620.000457
Other0.0009810.000978

dbNSFP

Source: dbNSFP

Disease
DISEASE: Sarcosinemia (SARCOS) [MIM:268900]: A metabolic disorder characterized by an increased concentration of sarcosine in plasma and an increased excretion of sarcosine in urine. Sarcosinemia is most probably a benign condition without significant clinical problems. Some reports have associated sarcosinemia with mental retardation and neurologic problems. {ECO:0000269|PubMed:10444331, ECO:0000269|PubMed:22825317}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Glycine, serine and threonine metabolism - Homo sapiens (human);3-Phosphoglycerate dehydrogenase deficiency;Non Ketotic Hyperglycinemia;Glycine and Serine Metabolism;sarcosine oncometabolite pathway ;Dimethylglycine Dehydrogenase Deficiency;Hyperglycinemia, non-ketotic;Dimethylglycine Dehydrogenase Deficiency;Sarcosinemia;Dihydropyrimidine Dehydrogenase Deficiency (DHPD);One carbon metabolism and related pathways;Metabolism of amino acids and derivatives;Metabolism;Choline catabolism;glycine betaine degradation;superpathway of choline degradation to L-serine;Glycine, serine, alanine and threonine metabolism (Consensus)

Recessive Scores

pRec
0.317

Intolerance Scores

loftool
0.115
rvis_EVS
1.41
rvis_percentile_EVS
94.81

Haploinsufficiency Scores

pHI
0.365
hipred
Y
hipred_score
0.755
ghis
0.441

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.887

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sardh
Phenotype

Gene ontology

Biological process
choline catabolic process;oxidation-reduction process;sarcosine catabolic process
Cellular component
cytoplasm;mitochondrion;mitochondrial matrix
Molecular function
sarcosine dehydrogenase activity;oxidoreductase activity