MRPS28

mitochondrial ribosomal protein S28, the group of Small subunit mitochondrial ribosomal proteins|Mitochondrial ribosomal proteins

Basic information

Region (hg38): 8:79918717-80030289

Links

ENSG00000147586 ∙ NCBI:28957 ∙ OMIM:611990 ∙ HGNC:14513 ∙ Uniprot:Q9Y2Q9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• combined oxidative phosphorylation deficiency 47 (Limited), mode of inheritance: AR
• combined oxidative phosphorylation deficiency 47 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Combined oxidative phosphorylation deficiency 47	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Audiologic/Otolaryngologic; Biochemical; Genitourinary; Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	30566640

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MRPS28 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPS28 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			14	2	3	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region				1		1
non coding				3		3
Total	0	0	15	7	3

Variants in MRPS28

This is a list of pathogenic ClinVar variants found in the MRPS28 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-79919003-T-C		not specified	Uncertain significance (Sep 06, 2022)
8-79919032-C-T		not specified	Uncertain significance (Mar 14, 2023)
8-79919059-A-T		not specified	Uncertain significance (Jul 19, 2022)
8-79919067-A-G		MRPS28-related disorder	Likely benign (Dec 12, 2021)
8-79919116-C-T		not specified	Uncertain significance (Dec 19, 2022)
8-79919122-C-T		not specified	Uncertain significance (Apr 26, 2024)
8-80003006-C-G		not specified	Uncertain significance (Sep 20, 2023)
8-80003038-T-C		Combined oxidative phosphorylation deficiency 47	Pathogenic (Jul 28, 2020)
8-80003077-T-G		MRPS28-related disorder	Uncertain significance (Aug 30, 2024)
8-80003084-T-C		not specified	Uncertain significance (Oct 30, 2023)
8-80003087-G-A		MRPS28-related disorder	Benign (Jan 28, 2020)
8-80003097-C-G			Likely benign (Oct 01, 2024)
8-80003129-G-A		MRPS28-related disorder	Benign (Nov 11, 2019)
8-80003165-C-T		MRPS28-related disorder	Likely benign (Sep 19, 2024)
8-80003171-T-C		not specified	Uncertain significance (Sep 22, 2022)
8-80003188-T-C		MRPS28-related disorder	Likely benign (Feb 28, 2022)
8-80030026-C-CGGGCTCCACCTTCTGTAGGGGCTCCACCTTCTGTAGGGGCTCCACCTTCTGTAGGGGCTCCACCTTCTGTAG		MRPS28-related disorder	Likely benign (Jul 24, 2022)
8-80030026-C-CGGGCTCCACCTTCTGTAG		MRPS28-related disorder	Likely benign (Dec 05, 2019)
8-80030026-C-CGGGCTCCACCTTCTGTAGGGGCTCCACCTTCTGTAGGGGCTCCACCTTCTGTAG			Likely benign (Nov 01, 2023)
8-80030034-A-C		not specified	Uncertain significance (Feb 07, 2024)
8-80030046-G-T		not specified	Uncertain significance (Apr 29, 2024)
8-80030053-C-T		not specified	Uncertain significance (Aug 21, 2023)
8-80030062-G-C		not specified	Uncertain significance (Jul 08, 2022)
8-80030065-G-A		not specified	Uncertain significance (Oct 06, 2021)
8-80030065-G-T		not specified	Uncertain significance (Aug 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPS28	protein_coding	protein_coding	ENST00000276585	3	111573

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000466	0.251	125699	0	48	125747	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0263	104	103	1.01	0.00000503	1196
Missense in Polyphen		28	36.596	0.76512		417
Synonymous	-1.23	51	41.0	1.24	0.00000191	389
Loss of Function	-0.398	6	5.04	1.19	2.10e-7	70

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00106	0.00105
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000164	0.000158
Middle Eastern	0.0000546	0.0000544
South Asian	0.000132	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Mitochondrial translation initiation;Translation;Metabolism of proteins;Mitochondrial translation elongation;Mitochondrial translation termination;Mitochondrial translation (Consensus)

Recessive Scores

• pRec: 0.0972

Intolerance Scores

• loftool: 0.787
• rvis_EVS: 0.9
• rvis_percentile_EVS: 89.39

Haploinsufficiency Scores

• pHI: 0.279
• hipred: N
• hipred_score: 0.144
• ghis: 0.426

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.248

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrps28

Gene ontology

• Biological process: biological_process;mitochondrial translational elongation;mitochondrial translational termination
• Cellular component: mitochondrion;mitochondrial inner membrane;mitochondrial small ribosomal subunit
• Molecular function: RNA binding