URGCP-MRPS24

URGCP-MRPS24 readthrough

Basic information

Region (hg38): 7:43866558-43906589

Links

ENSG00000270617 ∙ NCBI:100534592 ∙ ∙ HGNC:49188 ∙ ∙ ∙ 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 URGCP-MRPS24 gene.

• Inborn genetic diseases (33 variants)
• not provided (8 variants)
• Normal pregnancy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the URGCP-MRPS24 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			25	3	8	36
Total	0	0	26	3	8

Variants in URGCP-MRPS24

This is a list of pathogenic ClinVar variants found in the URGCP-MRPS24 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-43866722-T-C		not specified	Uncertain significance (Mar 11, 2022)
7-43866748-C-T		not specified	Uncertain significance (Nov 08, 2022)
7-43866749-G-C		not specified	Uncertain significance (Jul 02, 2024)
7-43866758-A-G		not specified	Uncertain significance (Oct 10, 2023)
7-43866766-A-G		not specified	Uncertain significance (Dec 27, 2023)
7-43866829-C-T		not specified	Uncertain significance (Jan 29, 2025)
7-43866839-C-T		not specified	Uncertain significance (Apr 01, 2024)
7-43866917-T-A		not specified	Uncertain significance (Dec 22, 2023)
7-43866923-T-C		not specified	Uncertain significance (Jun 11, 2024)
7-43866925-C-T		not specified	Uncertain significance (Jan 28, 2025)
7-43866926-G-A		not specified	Uncertain significance (Sep 13, 2023)
7-43866943-A-T		not specified	Uncertain significance (Apr 06, 2024)
7-43866965-C-T		not specified	Uncertain significance (Mar 31, 2023)
7-43868989-C-T		not specified	Uncertain significance (Feb 22, 2025)
7-43869045-C-T		not specified	Uncertain significance (Jan 19, 2024)
7-43869351-G-A		not specified	Uncertain significance (Oct 21, 2024)
7-43869371-C-T		not specified	Uncertain significance (Jan 03, 2022)
7-43876674-C-T		not specified	Uncertain significance (Feb 23, 2023)
7-43876690-T-G		not specified	Uncertain significance (May 07, 2024)
7-43876814-G-A			Benign (Dec 04, 2018)
7-43876825-C-T		not specified	Uncertain significance (Jan 24, 2024)
7-43876891-C-A		not specified	Uncertain significance (Mar 17, 2023)
7-43876947-A-G		not specified	Uncertain significance (Dec 10, 2024)
7-43877019-T-C		not specified	Uncertain significance (Mar 27, 2023)
7-43877037-G-A		not specified	Uncertain significance (Jun 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
URGCP-MRPS24	protein_coding	protein_coding	ENST00000603700	6	40032

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000525	0.709	125734	0	13	125747	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.858	45	64.4	0.699	0.00000317	683
Missense in Polyphen		4	8.349	0.4791		121
Synonymous	1.51	15	24.5	0.612	0.00000117	224
Loss of Function	0.857	6	8.73	0.687	4.78e-7	98

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000544
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000972	0.0000967
Middle Eastern	0.0000556	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.238

Gene Damage Prediction

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