RIMKLA

ribosomal modification protein rimK like family member A

Basic information

Region (hg38): 1:42380792-42424232

Previous symbols: [ "FAM80A" ]

Links

ENSG00000177181 ∙ NCBI:284716 ∙ OMIM:618949 ∙ HGNC:28725 ∙ Uniprot:Q8IXN7 ∙ 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 RIMKLA gene.

Variants pathogenicity by type

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

Variants in RIMKLA

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

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

Position	Type	Phenotype	Significance	ClinVar
1-42381036-C-G		not specified	Uncertain significance (Apr 17, 2023)
1-42381055-C-G		not specified	Uncertain significance (Aug 02, 2022)
1-42381056-T-G		not specified	Uncertain significance (Feb 14, 2023)
1-42399464-C-A		not specified	Uncertain significance (Apr 09, 2024)
1-42399539-A-G		not specified	Uncertain significance (May 25, 2022)
1-42399560-A-G		not specified	Uncertain significance (Dec 11, 2023)
1-42410043-C-T		not specified	Uncertain significance (Aug 10, 2021)
1-42410044-G-A		not specified	Uncertain significance (Dec 09, 2023)
1-42410146-G-A		not specified	Uncertain significance (Feb 22, 2023)
1-42414709-C-A		not specified	Uncertain significance (Feb 05, 2024)
1-42414817-A-G		not specified	Uncertain significance (Jul 14, 2021)
1-42414838-C-T		not specified	Uncertain significance (May 08, 2023)
1-42414874-G-A		not specified	Uncertain significance (Oct 04, 2022)
1-42414877-A-G		not specified	Uncertain significance (Dec 17, 2021)
1-42414891-A-G		not specified	Uncertain significance (Feb 27, 2023)
1-42414914-G-A		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RIMKLA	protein_coding	protein_coding	ENST00000431473	5	41784

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000631	0.915	125721	0	15	125736	0.0000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.22	160	210	0.763	0.0000119	2544
Missense in Polyphen		47	72.25	0.65052		882
Synonymous	1.63	65	83.9	0.774	0.00000492	802
Loss of Function	1.53	7	12.9	0.541	7.33e-7	158

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000883	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.0000340	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the synthesis of N-acetyl-L-aspartyl-L- glutamate (NAAG) and N-acetyl-L-aspartyl-L-glutamyl-L-glutamate. {ECO:0000250|UniProtKB:Q6PFX8}.
• Pathway: Alanine, aspartate and glutamate metabolism - Homo sapiens (human);Metabolism of amino acids and derivatives;Metabolism;Amino acid synthesis and interconversion (transamination) (Consensus)

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.207
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.75

Haploinsufficiency Scores

• pHI: 0.179
• hipred: Y
• hipred_score: 0.542
• ghis: 0.570

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.164

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rimkla

Gene ontology

• Biological process: cellular protein modification process;cellular amino acid biosynthetic process
• Cellular component: cytoplasm;cytosol
• Molecular function: ATP binding;metal ion binding;N-acetyl-L-aspartate-L-glutamate ligase activity