MDGA2

MAM domain containing glycosylphosphatidylinositol anchor 2, the group of I-set domain containing

Basic information

Region (hg38): 14:46840092-47675605

Previous symbols: [ "MAMDC1" ]

Links

ENSG00000139915 ∙ NCBI:161357 ∙ OMIM:611128 ∙ HGNC:19835 ∙ Uniprot:Q7Z553 ∙ 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 MDGA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MDGA2 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	2
missense			15		2	17
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	15	1	3

Variants in MDGA2

This is a list of pathogenic ClinVar variants found in the MDGA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-46841953-G-A		not specified	Uncertain significance (Dec 30, 2023)
14-46873576-A-C		not specified	Uncertain significance (Dec 12, 2023)
14-46874119-T-C		not specified	Uncertain significance (Oct 29, 2021)
14-46920047-C-T		not specified	Uncertain significance (Jan 23, 2024)
14-46920083-T-A		not specified	Uncertain significance (Jan 23, 2023)
14-46957483-C-G			Benign (Feb 01, 2018)
14-46957587-C-T		not specified	Uncertain significance (Jul 08, 2022)
14-47035224-C-T		not specified	Uncertain significance (Feb 07, 2023)
14-47061409-C-G		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
14-47061428-A-G		not specified	Uncertain significance (Jun 13, 2024)
14-47061528-C-T		not specified	Uncertain significance (Jul 20, 2022)
14-47096881-T-C		not specified	Uncertain significance (Feb 10, 2023)
14-47096942-G-A			Benign (Aug 04, 2017)
14-47131733-A-C		not specified	Uncertain significance (Jun 18, 2021)
14-47131743-A-G			Benign (Dec 31, 2019)
14-47131753-G-A		not specified	Uncertain significance (Apr 08, 2022)
14-47144093-T-C		not specified	Uncertain significance (Mar 25, 2024)
14-47144184-A-G		not specified	Uncertain significance (Jan 10, 2022)
14-47144272-A-T		not specified	Uncertain significance (Dec 04, 2023)
14-47218048-T-C		not specified	Uncertain significance (Feb 22, 2023)
14-47218058-C-A			Likely benign (Dec 13, 2017)
14-47301488-A-C		not specified	Uncertain significance (Feb 15, 2023)
14-47301496-T-C		Intellectual disability;Seizure	Uncertain significance (Mar 09, 2020)
14-47674517-C-CGT		Intellectual disability	Likely pathogenic (Oct 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MDGA2	protein_coding	protein_coding	ENST00000426342	13	835332

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000781	124784	0	7	124791	0.0000280

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.68	306	400	0.764	0.0000211	4724
Missense in Polyphen		78	165.25	0.47202		1923
Synonymous	0.830	125	137	0.910	0.00000720	1413
Loss of Function	5.14	4	38.3	0.104	0.00000209	453

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000354	0.0000353
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000167	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in cell-cell interactions. {ECO:0000250}.
• Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.260
• rvis_EVS: -1.02
• rvis_percentile_EVS: 8.1

Haploinsufficiency Scores

• pHI: 0.604
• hipred: N
• hipred_score: 0.481
• ghis: 0.449

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0524

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mdga2
• Phenotype: limbs/digits/tail phenotype; skeleton phenotype; embryo phenotype; growth/size/body region phenotype; craniofacial phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: mdga2a
• Affected structure: trigeminal motor nucleus
• Phenotype tag: abnormal
• Phenotype quality: mislocalised

Gene ontology

• Biological process: spinal cord motor neuron differentiation
• Cellular component: extracellular region;plasma membrane;anchored component of membrane