RRP7A

ribosomal RNA processing 7 homolog A, the group of Ribosomal biogenesis factors|UTPc subcomplex

Basic information

Region (hg38): 22:42507982-42519800

Links

ENSG00000189306 ∙ NCBI:27341 ∙ OMIM:619449 ∙ HGNC:24286 ∙ Uniprot:Q9Y3A4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• microcephaly 28, primary, autosomal recessive (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Microcephaly 28, primary, autosomal recessive	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	Neurologic	33199730

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RRP7A gene.

• not_specified (52 variants)
• not_provided (5 variants)
• Microcephaly_28,_primary,_autosomal_recessive (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RRP7A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015703.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3		3
missense	1		51			52
nonsense						0
start loss						0
frameshift			2			2
splice donor/acceptor (+/-2bp)						0
Total	1	0	53	3	0

Highest pathogenic variant AF is 0.0000013725178

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RRP7A	protein_coding	protein_coding	ENST00000323013	7	9835

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000238	0.929	125665	0	67	125732	0.000266

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.351	172	160	1.08	0.0000100	1747
Missense in Polyphen		31	35.219	0.8802		378
Synonymous	-0.366	68	64.3	1.06	0.00000390	541
Loss of Function	1.62	8	14.7	0.544	8.76e-7	156

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000539	0.000537
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000220	0.000218
Finnish	0.0000570	0.0000462
European (Non-Finnish)	0.000259	0.000246
Middle Eastern	0.000220	0.000218
South Asian	0.000606	0.000588
Other	0.000170	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human);rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Intolerance Scores

• loftool: 0.845
• rvis_EVS: 1.31
• rvis_percentile_EVS: 94

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.291
• ghis: 0.406

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.339

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rrp7a

Gene ontology

• Biological process: ribosomal small subunit assembly;blastocyst formation;rRNA processing
• Cellular component: nucleoplasm;cytoplasm;CURI complex;UTP-C complex
• Molecular function: RNA binding;protein binding