MAMDC4

MAM domain containing 4

Basic information

Region (hg38): 9:136850943-136860799

Links

ENSG00000177943 ∙ NCBI:158056 ∙ OMIM:617208 ∙ HGNC:24083 ∙ Uniprot:Q6UXC1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MAMDC4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAMDC4 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				4		4
missense			129	8		137
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	129	12	0

Variants in MAMDC4

This is a list of pathogenic ClinVar variants found in the MAMDC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-136853113-G-C		not specified	Uncertain significance (Jan 25, 2023)
9-136853119-G-T		not specified	Uncertain significance (Jun 10, 2022)
9-136853120-C-G		not specified	Uncertain significance (Jan 17, 2024)
9-136853158-G-A		not specified	Uncertain significance (Mar 01, 2023)
9-136853170-G-A		not specified	Uncertain significance (Apr 08, 2024)
9-136853324-C-T		not specified	Uncertain significance (Mar 27, 2023)
9-136853335-G-A		not specified	Uncertain significance (Feb 08, 2023)
9-136853350-G-A		not specified	Uncertain significance (Aug 09, 2021)
9-136853432-C-T		not specified	Uncertain significance (Feb 03, 2022)
9-136853435-A-T		not specified	Uncertain significance (Jun 06, 2022)
9-136853568-C-G		not specified	Uncertain significance (Aug 28, 2023)
9-136853574-G-A		not specified	Uncertain significance (Apr 12, 2022)
9-136853590-C-T		not specified	Uncertain significance (Sep 27, 2021)
9-136853617-G-A		not specified	Uncertain significance (Jun 12, 2023)
9-136853629-C-T		not specified	Uncertain significance (Apr 28, 2023)
9-136853791-C-T		not specified	Uncertain significance (Aug 15, 2023)
9-136853848-T-C		not specified	Uncertain significance (Oct 22, 2021)
9-136853887-C-T		not specified	Uncertain significance (Dec 07, 2021)
9-136854005-C-T		not specified	Uncertain significance (Dec 26, 2023)
9-136854017-C-T		not specified	Uncertain significance (Feb 21, 2024)
9-136854028-G-A		not specified	Uncertain significance (Oct 26, 2022)
9-136854211-C-T		not specified	Uncertain significance (Dec 13, 2023)
9-136854214-C-T		not specified	Uncertain significance (Dec 13, 2022)
9-136854228-C-T		not specified	Uncertain significance (Oct 13, 2023)
9-136854267-G-A		not specified	Uncertain significance (Mar 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAMDC4	protein_coding	protein_coding	ENST00000317446	27	9855

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.40e-51	2.51e-9	122153	24	3421	125598	0.0138

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.841	756	694	1.09	0.0000444	7177
Missense in Polyphen		307	270.33	1.1356		3078
Synonymous	-3.02	375	308	1.22	0.0000209	2407
Loss of Function	-0.710	74	67.7	1.09	0.00000363	642

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0202	0.0198
Ashkenazi Jewish	0.00615	0.00608
East Asian	0.00195	0.00191
Finnish	0.0239	0.0235
European (Non-Finnish)	0.0193	0.0189
Middle Eastern	0.00195	0.00191
South Asian	0.00561	0.00547
Other	0.0161	0.0159

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably involved in the sorting and selective transport of receptors and ligands across polarized epithelia. {ECO:0000250|UniProtKB:Q63191}.

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.979
• rvis_EVS: 1.89
• rvis_percentile_EVS: 97.28

Haploinsufficiency Scores

• pHI: 0.145
• hipred: N
• hipred_score: 0.146
• ghis: 0.452

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.146

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mamdc4

Gene ontology

• Biological process: protein transport
• Cellular component: integral component of membrane