MRPL38

mitochondrial ribosomal protein L38, the group of Large subunit mitochondrial ribosomal proteins|Mitochondrial ribosomal proteins

Basic information

Region (hg38): 17:75898644-75905093

Links

ENSG00000204316 ∙ NCBI:64978 ∙ OMIM:611844 ∙ HGNC:14033 ∙ Uniprot:Q96DV4 ∙ 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 MRPL38 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPL38 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			27	1		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	2	0

Variants in MRPL38

This is a list of pathogenic ClinVar variants found in the MRPL38 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-75898890-C-T		not specified	Uncertain significance (Mar 14, 2023)
17-75898891-G-A		not specified	Uncertain significance (Jul 20, 2021)
17-75898909-G-A		not specified	Uncertain significance (Oct 17, 2023)
17-75898914-C-T		not specified	Uncertain significance (Dec 08, 2023)
17-75898926-C-T		not specified	Uncertain significance (Aug 28, 2023)
17-75898942-G-A		not specified	Uncertain significance (Mar 01, 2024)
17-75898956-C-T		not specified	Uncertain significance (Jun 18, 2021)
17-75898957-G-A		not specified	Uncertain significance (Dec 03, 2021)
17-75898981-G-A		not specified	Uncertain significance (Dec 06, 2021)
17-75899170-G-T		not specified	Uncertain significance (Aug 11, 2022)
17-75899241-T-G		not specified	Uncertain significance (Jun 24, 2022)
17-75899532-C-T		not specified	Likely benign (Aug 12, 2021)
17-75899568-A-G		not specified	Uncertain significance (Jan 16, 2024)
17-75899603-C-T		not specified	Uncertain significance (Feb 14, 2023)
17-75899615-G-A		not specified	Uncertain significance (Nov 16, 2021)
17-75899622-G-A		not specified	Uncertain significance (Jan 03, 2024)
17-75899660-C-T		not specified	Uncertain significance (Jun 12, 2023)
17-75901248-T-C		not specified	Uncertain significance (Apr 30, 2024)
17-75901714-C-T		not specified	Uncertain significance (Dec 17, 2023)
17-75901715-G-A			Likely benign (Jan 01, 2023)
17-75901861-T-G		not specified	Uncertain significance (Jan 16, 2024)
17-75901897-G-A		not specified	Uncertain significance (Aug 09, 2021)
17-75902068-C-T		not specified	Uncertain significance (Jun 05, 2023)
17-75902074-T-C		not specified	Uncertain significance (Nov 17, 2022)
17-75902106-C-T		not specified	Uncertain significance (Dec 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPL38	protein_coding	protein_coding	ENST00000309352	9	11176

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.51e-9	0.593	125456	0	48	125504	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.192	222	230	0.964	0.0000147	2391
Missense in Polyphen		84	89.721	0.93624		940
Synonymous	-0.771	103	93.5	1.10	0.00000562	760
Loss of Function	1.20	16	22.1	0.724	0.00000121	229

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000121	0.000121
Ashkenazi Jewish	0.00	0.00
East Asian	0.000331	0.000326
Finnish	0.000128	0.0000925
European (Non-Finnish)	0.000309	0.000300
Middle Eastern	0.000331	0.000326
South Asian	0.0000668	0.0000653
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)

Intolerance Scores

• loftool: 0.654
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.69

Haploinsufficiency Scores

• pHI: 0.115
• hipred: N
• hipred_score: 0.204
• ghis: 0.564

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.871

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrpl38

Gene ontology

• Biological process: mitochondrial translational elongation;mitochondrial translational termination
• Cellular component: mitochondrion;mitochondrial inner membrane;mitochondrial large ribosomal subunit