MDGA1

MAM domain containing glycosylphosphatidylinositol anchor 1, the group of I-set domain containing

Basic information

Region (hg38): 6:37630678-37699306

Links

ENSG00000112139 ∙ NCBI:266727 ∙ OMIM:609626 ∙ HGNC:19267 ∙ Uniprot:Q8NFP4 ∙ 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 MDGA1 gene.

• Inborn genetic diseases (32 variants)
• not provided (6 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MDGA1 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				2	3	5
missense			33		1	34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	2	4

Variants in MDGA1

This is a list of pathogenic ClinVar variants found in the MDGA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-37637381-G-A		not specified	Uncertain significance (Jan 31, 2022)
6-37637435-G-A		not specified	Uncertain significance (Apr 26, 2023)
6-37637447-G-A		not specified	Uncertain significance (Dec 09, 2023)
6-37638221-C-A		not specified	Uncertain significance (Dec 15, 2023)
6-37638228-C-T		not specified	Uncertain significance (Apr 27, 2022)
6-37638260-A-G			Benign (Dec 31, 2019)
6-37638287-C-A			Benign (Dec 31, 2019)
6-37638288-G-A		not specified	Uncertain significance (May 17, 2023)
6-37638307-A-C		Acute megakaryoblastic leukemia;Mediastinal germ cell tumor	Uncertain significance (Oct 22, 2015)
6-37638555-G-A			Likely benign (Jan 01, 2023)
6-37638664-G-A		not specified	Uncertain significance (Dec 02, 2022)
6-37643841-G-A		not specified	Uncertain significance (Oct 05, 2023)
6-37643865-G-T		not specified	Uncertain significance (Nov 09, 2022)
6-37643875-G-C		not specified	Uncertain significance (Dec 12, 2023)
6-37643877-G-A		not specified	Uncertain significance (Feb 05, 2024)
6-37643896-G-A		not specified	Uncertain significance (Jan 03, 2024)
6-37643905-G-T		not specified	Uncertain significance (Nov 09, 2021)
6-37643938-A-G		not specified	Uncertain significance (Sep 06, 2022)
6-37644563-G-A		not specified	Uncertain significance (Jul 15, 2015)
6-37644649-T-C		not specified	Uncertain significance (Nov 06, 2023)
6-37646219-G-A		not specified	Uncertain significance (Oct 22, 2021)
6-37646228-T-C		not specified	Uncertain significance (Jun 28, 2023)
6-37646268-C-G			Benign (Feb 25, 2018)
6-37646349-C-A		not specified	Uncertain significance (Nov 29, 2023)
6-37649032-C-A		not specified	Uncertain significance (Aug 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MDGA1	protein_coding	protein_coding	ENST00000434837	17	66799

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.976	0.0243	124651	0	18	124669	0.0000722

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.57	404	578	0.699	0.0000365	6078
Missense in Polyphen		182	286.05	0.63624		3036
Synonymous	0.418	239	247	0.966	0.0000161	1979
Loss of Function	5.03	7	42.3	0.166	0.00000227	457

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000584	0.0000584
Ashkenazi Jewish	0.0000994	0.0000994
East Asian	0.000112	0.000111
Finnish	0.0000472	0.0000464
European (Non-Finnish)	0.000109	0.000106
Middle Eastern	0.000112	0.000111
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for radial migration of cortical neurons in the superficial layer of the neocortex (By similarity). Plays a role in the formation or maintenance of inhibitory synapses. May function by inhibiting the activity of NLGN2. {ECO:0000250, ECO:0000269|PubMed:23248271}.
• Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Intolerance Scores

• rvis_EVS: -1.13
• rvis_percentile_EVS: 6.56

Haploinsufficiency Scores

• pHI: 0.154
• hipred: Y
• hipred_score: 0.837
• ghis: 0.635

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.463

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mdga1
• Phenotype: cellular phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: neuron migration;brain development;spinal cord association neuron differentiation;regulation of synaptic membrane adhesion;regulation of presynapse assembly
• Cellular component: extracellular region;extracellular space;plasma membrane;anchored component of plasma membrane;GABA-ergic synapse
• Molecular function: molecular_function