MRPL28

mitochondrial ribosomal protein L28, the group of Large subunit mitochondrial ribosomal proteins|Mitochondrial ribosomal proteins

Basic information

Region (hg38): 16:366968-371289

Previous symbols: [ "MAAT1" ]

Links

ENSG00000086504 ∙ NCBI:10573 ∙ OMIM:604853 ∙ HGNC:14484 ∙ Uniprot:Q13084 ∙ 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 MRPL28 gene.

• Inborn genetic diseases (12 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPL28 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
missense			12			12
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	0	1

Variants in MRPL28

This is a list of pathogenic ClinVar variants found in the MRPL28 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-367759-G-C		not specified	Uncertain significance (Mar 23, 2023)
16-367765-G-C		not specified	Uncertain significance (Apr 28, 2022)
16-368365-T-G		not specified	Uncertain significance (Dec 26, 2023)
16-368381-C-T		Oromandibular-limb hypogenesis spectrum	Likely benign (Aug 12, 2016)
16-368530-G-A		not specified	Uncertain significance (Jun 22, 2021)
16-368542-C-T		not specified	Uncertain significance (Dec 21, 2023)
16-368574-C-T		not specified	Uncertain significance (Jan 04, 2024)
16-368575-G-A		not specified	Uncertain significance (Sep 12, 2023)
16-368589-C-T		not specified	Uncertain significance (Dec 09, 2023)
16-368611-T-G		not specified	Uncertain significance (Sep 14, 2022)
16-369086-G-C			Benign (Apr 16, 2018)
16-369123-A-G		not specified	Uncertain significance (Feb 28, 2024)
16-369186-T-C		not specified	Uncertain significance (Feb 05, 2024)
16-369939-T-G		not specified	Uncertain significance (Jan 23, 2023)
16-369957-C-T		not specified	Uncertain significance (Jul 14, 2022)
16-369991-C-G		not specified	Uncertain significance (Dec 20, 2023)
16-370005-G-A		not specified	Uncertain significance (May 18, 2022)
16-370032-C-T		not specified	Uncertain significance (Jan 03, 2024)
16-370043-C-G		Oromandibular-limb hypogenesis spectrum	Likely benign (Aug 12, 2016)
16-370060-G-C		not specified	Uncertain significance (Aug 02, 2021)
16-370061-T-G		not specified	Uncertain significance (May 09, 2023)
16-370107-G-A		not specified	Uncertain significance (May 31, 2023)
16-370194-A-T		not specified	Uncertain significance (May 16, 2023)
16-370197-C-G		not specified	Uncertain significance (Feb 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPL28	protein_coding	protein_coding	ENST00000199706	5	3144

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.00e-7	0.266	125666	0	61	125727	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.30	200	154	1.30	0.00000932	1633
Missense in Polyphen		53	52.678	1.0061		537
Synonymous	-4.86	120	68.8	1.75	0.00000416	511
Loss of Function	0.355	11	12.3	0.891	6.95e-7	130

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000556	0.000556
Ashkenazi Jewish	0.00122	0.00119
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000232	0.000229
Middle Eastern	0.000164	0.000163
South Asian	0.0000677	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Ribosome - Homo sapiens (human);Mitochondrial translation initiation;Translation;Metabolism of proteins;Mitochondrial translation elongation;Mitochondrial translation termination;Mitochondrial translation (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.702
• rvis_EVS: 1.02
• rvis_percentile_EVS: 90.98

Haploinsufficiency Scores

• pHI: 0.109
• hipred: N
• hipred_score: 0.197
• ghis: 0.397

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.910

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrpl28

Gene ontology

• Biological process: translation;mitochondrial translational elongation;mitochondrial translational termination
• Cellular component: mitochondrion;mitochondrial inner membrane;mitochondrial ribosome;mitochondrial large ribosomal subunit;cytosol
• Molecular function: RNA binding;structural constituent of ribosome;protein binding