GSDMA

gasdermin A, the group of Gasdermins

Basic information

Region (hg38): 17:39953262-39977768

Previous symbols: [ "GSDM", "GSDM1" ]

Links

ENSG00000167914 ∙ NCBI:284110 ∙ OMIM:611218 ∙ HGNC:13311 ∙ Uniprot:Q96QA5 ∙ 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 GSDMA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GSDMA 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			16	2		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	16	3	1

Variants in GSDMA

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

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

Position	Type	Phenotype	Significance	ClinVar
17-39965728-A-G		not specified	Uncertain significance (Jun 10, 2022)
17-39965800-T-C		not specified	Uncertain significance (Oct 26, 2022)
17-39965842-G-A		not specified	Uncertain significance (Jun 05, 2023)
17-39965896-C-T		not specified	Uncertain significance (Dec 28, 2023)
17-39966356-C-T		not specified	Uncertain significance (Oct 03, 2022)
17-39966381-T-C			Likely benign (Feb 01, 2023)
17-39970544-T-A		not specified	Uncertain significance (Oct 30, 2023)
17-39970658-AACAC-A		not specified	Benign (Mar 29, 2016)
17-39971528-C-T		not specified	Uncertain significance (Jan 16, 2024)
17-39971569-G-A		not specified	Likely benign (Aug 22, 2023)
17-39972607-G-T		not specified	Likely benign (Jun 03, 2022)
17-39974273-G-A		not specified	Uncertain significance (May 25, 2022)
17-39974288-G-T		not specified	Uncertain significance (Jun 29, 2023)
17-39974311-G-C		not specified	Uncertain significance (Sep 12, 2023)
17-39974377-C-T		not specified	Uncertain significance (Dec 19, 2022)
17-39974939-G-C		not specified	Uncertain significance (Mar 22, 2023)
17-39974948-C-T		not specified	Uncertain significance (Aug 02, 2022)
17-39975983-G-A		not specified	Uncertain significance (Dec 14, 2022)
17-39976847-T-C		not specified	Uncertain significance (Jun 26, 2023)
17-39976981-G-A		not specified	Uncertain significance (Jun 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GSDMA	protein_coding	protein_coding	ENST00000301659	11	14794

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.62e-16	0.00665	124434	1	211	124646	0.000851

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.277	224	236	0.949	0.0000130	2823
Missense in Polyphen		79	80.85	0.97712		1010
Synonymous	1.02	88	101	0.871	0.00000587	898
Loss of Function	-0.0841	24	23.6	1.02	0.00000145	250

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00113	0.00109
Ashkenazi Jewish	0.00	0.00
East Asian	0.000979	0.000890
Finnish	0.0000947	0.0000928
European (Non-Finnish)	0.000573	0.000540
Middle Eastern	0.000979	0.000890
South Asian	0.00357	0.00340
Other	0.000343	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May promote pyroptosis (Probable). Upon cleavage in vitro of genetically engineered GSDMA, the released N-terminal moiety binds to some types of lipids, such as possibly phosphatidylinositol (4,5)-bisphosphate. Homooligomerizes within the membrane and forms pores of 10 -15 nanometers (nm) of inner diameter, triggering cell death. Also binds to bacterial and mitochondrial lipids, including cardiolipin, and exhibits bactericidal activity (PubMed:27281216). The physiological relevance of these observations is unknown (Probable). {ECO:0000269|PubMed:27281216, ECO:0000305, ECO:0000305|PubMed:17471240, ECO:0000305|PubMed:27281216}.

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.907
• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.41

Haploinsufficiency Scores

• pHI: 0.211
• hipred: N
• hipred_score: 0.153
• ghis: 0.462

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.190

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gsdma

Gene ontology

• Biological process: apoptotic process;pyroptosis
• Cellular component: cytosol;plasma membrane;perinuclear region of cytoplasm
• Molecular function: phosphatidylserine binding;phosphatidylinositol-4,5-bisphosphate binding;phosphatidylinositol-4-phosphate binding