MDH1B

malate dehydrogenase 1B

Basic information

Region (hg38): 2:206737762-206765328

Links

ENSG00000138400 ∙ NCBI:130752 ∙ ∙ HGNC:17836 ∙ Uniprot:Q5I0G3 ∙ 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 MDH1B gene.

• Inborn genetic diseases (25 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MDH1B 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				1		1
missense			24	2		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	3	0

Variants in MDH1B

This is a list of pathogenic ClinVar variants found in the MDH1B region.

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

Position	Type	Phenotype	Significance	ClinVar
2-206739654-C-A		not specified	Likely benign (Jul 25, 2023)
2-206745631-A-G		not specified	Uncertain significance (Jan 08, 2024)
2-206746330-A-C		not specified	Uncertain significance (Feb 14, 2023)
2-206746410-C-T			Likely benign (Dec 01, 2022)
2-206749050-C-G		not specified	Uncertain significance (Jan 09, 2024)
2-206749158-C-A		not specified	Uncertain significance (Feb 28, 2023)
2-206750958-G-A		not specified	Uncertain significance (Jan 17, 2024)
2-206750979-C-A		not specified	Uncertain significance (Jan 23, 2024)
2-206751028-C-A		not specified	Uncertain significance (Sep 07, 2022)
2-206751066-T-C		not specified	Uncertain significance (Apr 18, 2023)
2-206755068-A-C		not specified	Uncertain significance (May 09, 2022)
2-206755068-A-G		not specified	Uncertain significance (Sep 16, 2021)
2-206755071-G-A		not specified	Uncertain significance (Feb 14, 2023)
2-206755104-G-A		not specified	Uncertain significance (Mar 06, 2023)
2-206755140-A-T		not specified	Uncertain significance (Jul 17, 2023)
2-206755156-C-T		not specified	Uncertain significance (May 04, 2023)
2-206755170-G-A		not specified	Uncertain significance (Oct 06, 2023)
2-206755207-G-C		not specified	Uncertain significance (Apr 05, 2023)
2-206755216-G-A		not specified	Uncertain significance (Aug 16, 2021)
2-206755291-C-T		not specified	Uncertain significance (May 24, 2023)
2-206755302-C-T		not specified	Uncertain significance (May 09, 2023)
2-206755324-T-C		not specified	Uncertain significance (Feb 22, 2023)
2-206755341-C-T		not specified	Uncertain significance (Mar 07, 2023)
2-206755342-G-A		not specified	Uncertain significance (Jul 14, 2022)
2-206755387-T-C		not specified	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MDH1B	protein_coding	protein_coding	ENST00000374412	12	27785

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.87e-14	0.117	125683	0	65	125748	0.000258

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.448	264	285	0.925	0.0000147	3398
Missense in Polyphen		57	59.954	0.95073		755
Synonymous	0.197	100	103	0.975	0.00000560	982
Loss of Function	0.823	23	27.7	0.831	0.00000134	334

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000729	0.000729
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000318	0.000264
Middle Eastern	0.000163	0.000163
South Asian	0.000491	0.000490
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0916

Intolerance Scores

• loftool: 0.924
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.49

Haploinsufficiency Scores

• pHI: 0.137
• hipred: N
• hipred_score: 0.146
• ghis: 0.522

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.324

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mdh1b

Gene ontology

• Biological process: carbohydrate metabolic process;tricarboxylic acid cycle;oxaloacetate metabolic process;malate metabolic process;NADH metabolic process
• Molecular function: L-malate dehydrogenase activity