SARDH

sarcosine dehydrogenase

Basic information

Region (hg38): 9:133663560-133739955

Previous symbols: [ "DMGDHL1" ]

Links

ENSG00000123453 ∙ NCBI:1757 ∙ OMIM:604455 ∙ HGNC:10536 ∙ Uniprot:Q9UL12 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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.

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				13	13	26
missense			65	10	7	82
nonsense						0
start loss				1		1
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				3	1	4
non coding						0
Total	0	1	65	24	20

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)
9-133663932-G-A		not specified	Uncertain significance (Sep 17, 2021)
9-133664010-G-A		not specified	Uncertain significance (Dec 19, 2022)
9-133666739-C-T		not specified	Uncertain significance (Aug 26, 2022)
9-133666754-T-C		not specified	Likely benign (Dec 02, 2022)
9-133666765-G-A			Likely benign (Aug 01, 2022)
9-133666768-G-A		SARDH-related disorder	Likely benign (Apr 29, 2019)
9-133666770-C-T		not specified	Uncertain significance (Mar 06, 2023)
9-133666782-C-T		not specified	Likely benign (Jul 09, 2021)
9-133666783-G-C		not specified	Uncertain significance (Jul 27, 2021)
9-133666831-G-A		SARDH-related disorder	Likely benign (Dec 24, 2019)
9-133670611-C-T		not specified	Uncertain significance (Jan 07, 2022)
9-133670612-G-A		not specified	Uncertain significance (Jun 22, 2023)
9-133670615-G-A		not specified	Uncertain significance (Jul 13, 2021)
9-133670624-C-T			Benign (Dec 31, 2019)
9-133670630-G-A		not specified	Uncertain significance (Jul 20, 2021)
9-133670635-T-C		not specified	Uncertain significance (Aug 23, 2021)
9-133670668-G-T		not specified	Uncertain significance (May 07, 2024)
9-133670733-C-T			Benign (Feb 01, 2024)
9-133670734-G-A			Likely benign (Jul 01, 2023)
9-133670747-G-A		not specified	Uncertain significance (Nov 13, 2023)
9-133671557-G-A		SARDH-related disorder	Benign (Oct 17, 2019)
9-133671564-C-T		not specified	Uncertain significance (Aug 08, 2022)
9-133671600-G-A		not specified	Uncertain significance (Mar 30, 2024)
9-133671601-C-T		not specified	Uncertain significance (Mar 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SARDH	protein_coding	protein_coding	ENST00000371872	20	76396

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.27e-16	0.917	125455	0	293	125748	0.00117

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.679	561	608	0.923	0.0000407	5870
Missense in Polyphen		194	245.77	0.78936		2404
Synonymous	0.102	262	264	0.992	0.0000192	1872
Loss of Function	2.23	32	48.8	0.655	0.00000285	471

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00203	0.00195
Ashkenazi Jewish	0.00190	0.00189
East Asian	0.000502	0.000489
Finnish	0.00334	0.00329
European (Non-Finnish)	0.00112	0.00111
Middle Eastern	0.000502	0.000489
South Asian	0.000462	0.000457
Other	0.000981	0.000978

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

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

Mouse Genome Informatics

• Gene name: Sardh

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