GAPDHS

glyceraldehyde-3-phosphate dehydrogenase, spermatogenic

Basic information

Region (hg38): 19:35533454-35545319

Previous symbols: [ "GAPDS" ]

Links

ENSG00000105679 ∙ NCBI:26330 ∙ OMIM:609169 ∙ HGNC:24864 ∙ Uniprot:O14556 ∙ 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 GAPDHS gene.

• Inborn genetic diseases (21 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GAPDHS 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			21		1	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	0	2

Variants in GAPDHS

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

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

Position	Type	Phenotype	Significance	ClinVar
19-35533546-G-A		not specified	Uncertain significance (May 24, 2023)
19-35536831-C-A		not specified	Uncertain significance (Aug 08, 2022)
19-35536831-C-T		not specified	Uncertain significance (Mar 14, 2024)
19-35536854-G-C		not specified	Uncertain significance (Oct 20, 2021)
19-35536860-C-G		not specified	Uncertain significance (Jan 26, 2022)
19-35536915-C-T		not specified	Uncertain significance (Jan 04, 2022)
19-35536942-C-T		not specified	Uncertain significance (Sep 14, 2023)
19-35536965-C-T		not specified	Uncertain significance (Jan 17, 2024)
19-35536966-G-A		not specified	Uncertain significance (Oct 25, 2023)
19-35538308-T-C		not specified	Uncertain significance (Mar 30, 2022)
19-35538324-G-A		not specified	Uncertain significance (Sep 16, 2021)
19-35538335-C-T		not specified	Uncertain significance (Jun 06, 2023)
19-35538591-G-T		not specified	Uncertain significance (Aug 02, 2021)
19-35542353-G-A		not specified	Uncertain significance (Nov 21, 2022)
19-35542365-G-A		not specified	Uncertain significance (Aug 16, 2021)
19-35542375-C-G		not specified	Uncertain significance (Aug 03, 2022)
19-35542529-G-A		not specified	Uncertain significance (Mar 16, 2022)
19-35542550-A-G			Benign (Mar 29, 2018)
19-35543359-C-T		not specified	Uncertain significance (Jan 04, 2022)
19-35543382-G-A		not specified	Uncertain significance (Jul 09, 2021)
19-35543398-C-T		not specified	Uncertain significance (Dec 13, 2022)
19-35543404-G-A		not specified	Uncertain significance (Dec 15, 2022)
19-35543454-G-T		not specified	Uncertain significance (Feb 27, 2024)
19-35543456-G-A			Benign (Mar 29, 2018)
19-35543712-T-C		not specified	Uncertain significance (May 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GAPDHS	protein_coding	protein_coding	ENST00000222286	11	11905

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000334	0.988	125696	0	52	125748	0.000207

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.339	252	268	0.942	0.0000163	2631
Missense in Polyphen		127	145.23	0.87446		1381
Synonymous	2.87	71	109	0.650	0.00000712	846
Loss of Function	2.25	11	22.5	0.488	0.00000126	232

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000777	0.000774
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.000489	0.000489
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000489	0.000489
South Asian	0.000165	0.000163
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play an important role in regulating the switch between different pathways for energy production during spermiogenesis and in the spermatozoon. Required for sperm motility and male fertility (By similarity). {ECO:0000250}.
• Pathway: Glycolysis / Gluconeogenesis - Homo sapiens (human);Glycolysis and Gluconeogenesis;Metabolism of carbohydrates;Metabolism of proteins;Glycolysis Gluconeogenesis;Chaperonin-mediated protein folding;Metabolism;Association of TriC/CCT with target proteins during biosynthesis;Glycolysis;gluconeogenesis;Protein folding;glycolysis;superpathway of conversion of glucose to acetyl CoA and entry into the TCA cycle;Gluconeogenesis;Glucose metabolism (Consensus)

Recessive Scores

• pRec: 0.271

Intolerance Scores

• loftool: 0.771
• rvis_EVS: -0.13
• rvis_percentile_EVS: 43.91

Haploinsufficiency Scores

• pHI: 0.0755
• hipred: Y
• hipred_score: 0.662
• ghis: 0.458

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.927

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gapdhs
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: gluconeogenesis;glycolytic process;flagellated sperm motility;positive regulation of glycolytic process;canonical glycolysis
• Cellular component: nucleus;cytosol
• Molecular function: glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity;protein binding;NADP binding;NAD binding