MALSU1

mitochondrial assembly of ribosomal large subunit 1

Basic information

Region (hg38): 7:23298738-23311729

Previous symbols: [ "C7orf30" ]

Links

ENSG00000156928 ∙ NCBI:115416 ∙ OMIM:614624 ∙ HGNC:21721 ∙ Uniprot:Q96EH3 ∙ 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 MALSU1 gene.

• Inborn genetic diseases (13 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MALSU1 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						0
missense			12	1		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	0

Variants in MALSU1

This is a list of pathogenic ClinVar variants found in the MALSU1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-23299365-G-A		not specified	Uncertain significance (Dec 06, 2023)
7-23299369-G-T		not specified	Uncertain significance (May 04, 2022)
7-23299386-G-A		not specified	Uncertain significance (Feb 05, 2024)
7-23299386-G-C		not specified	Uncertain significance (Dec 13, 2022)
7-23299401-C-T		not specified	Uncertain significance (Aug 17, 2021)
7-23299408-C-A		not specified	Uncertain significance (Nov 30, 2022)
7-23299417-C-T		not specified	Uncertain significance (May 26, 2022)
7-23299432-C-T		not specified	Uncertain significance (Jan 31, 2024)
7-23299440-G-A		not specified	Uncertain significance (Oct 02, 2023)
7-23299440-G-C		not specified	Uncertain significance (Apr 07, 2022)
7-23299444-A-C		not specified	Uncertain significance (Sep 22, 2023)
7-23299474-G-C		not specified	Uncertain significance (Dec 13, 2022)
7-23299482-G-A		not specified	Uncertain significance (Aug 21, 2023)
7-23299498-G-A		not specified	Uncertain significance (Jul 05, 2023)
7-23299518-A-G		not specified	Uncertain significance (Jan 08, 2024)
7-23299539-A-G		not specified	Likely benign (Nov 08, 2022)
7-23299596-T-C		not specified	Uncertain significance (May 17, 2023)
7-23300868-A-G		not specified	Uncertain significance (Nov 17, 2023)
7-23300868-A-T		not specified	Uncertain significance (Dec 21, 2023)
7-23307893-A-G		not specified	Uncertain significance (Oct 10, 2023)
7-23309454-A-C		not specified	Uncertain significance (Jun 24, 2022)
7-23309460-C-T		not specified	Uncertain significance (Aug 22, 2023)
7-23309461-C-G		not specified	Uncertain significance (Feb 13, 2024)
7-23309488-T-C		not specified	Uncertain significance (Mar 01, 2024)
7-23309506-C-T		not specified	Uncertain significance (Oct 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MALSU1	protein_coding	protein_coding	ENST00000466681	4	12991

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.68e-11	0.00852	125658	0	90	125748	0.000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.21	177	137	1.29	0.00000670	1499
Missense in Polyphen		44	37.876	1.1617		486
Synonymous	-2.69	78	53.1	1.47	0.00000263	475
Loss of Function	-1.29	14	9.68	1.45	4.95e-7	109

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000889	0.000889
Ashkenazi Jewish	0.000896	0.000893
East Asian	0.000273	0.000272
Finnish	0.0000482	0.0000462
European (Non-Finnish)	0.000320	0.000316
Middle Eastern	0.000273	0.000272
South Asian	0.000298	0.000294
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for normal mitochondrial ribosome function and mitochondrial translation (PubMed:22238375, PubMed:23171548). May play a role in ribosome biogenesis by preventing premature association of the 28S and 39S ribosomal subunits (Probable). Interacts with mitochondrial ribosomal protein L14 (MRPL14), probably blocking formation of intersubunit bridge B8, preventing association of the 28S and 39S ribosomal subunits (Probable). Addition to isolated mitochondrial ribosomal subunits partially inhibits translation, probably by interfering with the association of the 28S and 39S ribosomal subunits and the formation of functional ribosomes (Probable). May also participate in the assembly and/or regulation of the stability of the large subunit of the mitochondrial ribosome (PubMed:22238376, PubMed:23171548). May function as a ribosomal silencing factor (Probable). {ECO:0000269|PubMed:22238375, ECO:0000269|PubMed:22238376, ECO:0000269|PubMed:23171548, ECO:0000305|PubMed:22829778, ECO:0000305|PubMed:28892042}.

Recessive Scores

• pRec: 0.0906

Intolerance Scores

• rvis_EVS: -0.52
• rvis_percentile_EVS: 21.2

Haploinsufficiency Scores

• pHI: 0.0342
• hipred: N
• hipred_score: 0.144
• ghis: 0.591

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Malsu1

Gene ontology

• Biological process: negative regulation of translation;ribosomal large subunit biogenesis;negative regulation of mitochondrial translation;negative regulation of ribosome biogenesis
• Cellular component: mitochondrion;mitochondrial large ribosomal subunit;cytosol
• Molecular function: protein binding;ribosomal large subunit binding