MALRD1

MAM and LDL receptor class A domain containing 1

Basic information

Region (hg38): 10:19048801-19790401

Previous symbols: [ "C10orf112" ]

Links

ENSG00000204740 ∙ NCBI:340895 ∙ OMIM:617715 ∙ HGNC:24331 ∙ Uniprot:Q5VYJ5 ∙ 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 MALRD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MALRD1 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	4	5
missense					5	5
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	0	1	10

Variants in MALRD1

This is a list of pathogenic ClinVar variants found in the MALRD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-19103996-A-G			Benign (Jun 06, 2018)
10-19128252-T-C			Benign (Apr 26, 2018)
10-19128279-G-A			Likely benign (Jun 19, 2018)
10-19136602-A-G			Benign (Jun 10, 2018)
10-19136775-A-G			Benign (Jun 23, 2018)
10-19165736-T-G			Benign (Jun 01, 2023)
10-19165786-G-A			Benign (Jun 20, 2018)
10-19203773-C-T			Benign (Jun 20, 2018)
10-19450384-G-C			Benign (Apr 17, 2018)
10-19491622-A-G			Benign (Jun 08, 2018)
10-19615941-ATTT-A			Benign (Jan 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MALRD1	protein_coding	protein_coding	ENST00000377266	25	586552

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.38e-21	0.934	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.296	727	750	0.970	0.0000381	9766
Missense in Polyphen		209	239.98	0.87091		3353
Synonymous	0.244	269	274	0.981	0.0000144	2766
Loss of Function	2.51	42	63.6	0.660	0.00000311	835

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Enhances production and/or transport of FGF19 and thus has a role in regulation of bile acid synthesis. {ECO:0000269|PubMed:23747249}.

Recessive Scores

• pRec: 0.0811

Haploinsufficiency Scores

• pHI: 0.143

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Malrd1
• Phenotype: homeostasis/metabolism phenotype; liver/biliary system phenotype

Gene ontology

• Biological process: cholesterol homeostasis;negative regulation of bile acid biosynthetic process
• Cellular component: Golgi apparatus;integral component of membrane;cytoplasmic vesicle membrane