MAMDC2

MAM domain containing 2

Basic information

Region (hg38): 9:70043847-70226972

Links

ENSG00000165072 ∙ NCBI:256691 ∙ OMIM:612879 ∙ HGNC:23673 ∙ Uniprot:Q7Z304 ∙ 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 MAMDC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAMDC2 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	2
missense			33	3	2	38
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	3	4

Variants in MAMDC2

This is a list of pathogenic ClinVar variants found in the MAMDC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-70044607-G-A		Malignant tumor of prostate	Uncertain significance (-)
9-70044628-G-A		not specified	Uncertain significance (Feb 13, 2024)
9-70044667-G-T		not specified	Uncertain significance (Sep 16, 2021)
9-70108217-A-G		not specified	Uncertain significance (Jul 11, 2023)
9-70108234-T-A		not specified	Uncertain significance (Apr 19, 2024)
9-70108300-T-C		not specified	Uncertain significance (Dec 08, 2023)
9-70108372-A-G		not specified	Likely benign (Feb 13, 2024)
9-70108386-T-G		not specified	Uncertain significance (Dec 18, 2023)
9-70108408-T-C		not specified	Uncertain significance (Aug 02, 2021)
9-70109748-G-C		not specified	Uncertain significance (Aug 08, 2023)
9-70109792-G-A		not specified	Uncertain significance (Nov 09, 2022)
9-70113081-C-T		not specified	Uncertain significance (Jun 07, 2024)
9-70113084-A-G		not specified	Uncertain significance (Jun 06, 2023)
9-70126233-A-G		not specified	Uncertain significance (Jun 30, 2022)
9-70126332-G-A		not specified	Uncertain significance (Dec 12, 2023)
9-70126337-A-C		not specified	Uncertain significance (Mar 07, 2023)
9-70126363-A-G		not specified	Likely benign (Sep 14, 2022)
9-70126401-C-G		not specified	Uncertain significance (Jun 16, 2024)
9-70131576-A-T		not specified	Uncertain significance (Feb 03, 2022)
9-70131610-C-G		not specified	Uncertain significance (Feb 03, 2022)
9-70140160-C-T		not specified	Uncertain significance (Sep 17, 2021)
9-70140225-G-C		not specified	Uncertain significance (Sep 20, 2023)
9-70140228-T-G		not specified	Uncertain significance (Feb 06, 2023)
9-70140256-T-C		not specified	Uncertain significance (Feb 15, 2023)
9-70140262-G-A		not specified	Uncertain significance (May 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAMDC2	protein_coding	protein_coding	ENST00000377182	14	183390

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.10e-10	0.995	125697	0	51	125748	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.275	351	366	0.960	0.0000182	4482
Missense in Polyphen		127	149.14	0.85153		1859
Synonymous	0.467	127	134	0.949	0.00000656	1265
Loss of Function	2.64	22	40.0	0.550	0.00000204	455

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000550	0.000550
Ashkenazi Jewish	0.00	0.00
East Asian	0.000386	0.000381
Finnish	0.0000930	0.0000924
European (Non-Finnish)	0.000187	0.000185
Middle Eastern	0.000386	0.000381
South Asian	0.000369	0.000359
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.829
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.49

Haploinsufficiency Scores

• pHI: 0.243
• hipred: N
• hipred_score: 0.492
• ghis: 0.497

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.298

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mamdc2

Gene ontology

• Cellular component: extracellular region;endoplasmic reticulum;membrane