C4orf50

chromosome 4 open reading frame 50, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 4:5897373-6200555

Links

ENSG00000181215 ∙ NCBI:389197 ∙ ∙ HGNC:33766 ∙ Uniprot:Q6ZRC1 ∙ 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 C4orf50 gene.

• not provided (23 variants)
• Inborn genetic diseases (18 variants)
• Intellectual disability (1 variants)
• Smith-Magenis Syndrome-like (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C4orf50 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				4		4
missense					1	1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1	1		2
splice region						0
non coding				1	1	2
Total	0	0	1	6	2

Variants in C4orf50

This is a list of pathogenic ClinVar variants found in the C4orf50 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-5988662-G-A			Likely benign (Apr 01, 2022)
4-5988779-G-A			Likely benign (Sep 01, 2022)
4-5989379-G-A			Likely benign (Apr 01, 2022)
4-5990543-C-T			Likely benign (Apr 01, 2022)
4-6008486-C-T			Benign (Jul 01, 2023)
4-6029725-C-T			Likely benign (Mar 29, 2018)
4-6036057-C-T			Benign (Dec 31, 2019)
4-6036072-C-T			Benign (Dec 31, 2019)
4-6042198-G-A			Benign (Jun 10, 2018)
4-6054098-G-A			Benign (Dec 31, 2019)
4-6054100-C-G		Smith-Magenis Syndrome-like	Pathogenic (Aug 15, 2016)
4-6056726-T-C		not specified	Uncertain significance (May 09, 2022)
4-6060504-G-A		not specified	Uncertain significance (Jun 09, 2022)
4-6062330-G-A			Likely benign (Jun 25, 2018)
4-6062396-G-C			Likely benign (Apr 11, 2018)
4-6062401-G-T			Uncertain significance (Feb 12, 2021)
4-6062408-G-A			Benign (Apr 04, 2018)
4-6062442-T-C		Intellectual disability	Uncertain significance (Aug 01, 2017)
4-6064920-G-A		not specified	Uncertain significance (Jan 03, 2024)
4-6064991-T-C			Likely benign (Oct 16, 2018)
4-6065017-C-T			Likely benign (Dec 04, 2017)
4-6078946-G-A		not specified	Uncertain significance (Oct 26, 2022)
4-6078979-C-T		not specified	Uncertain significance (Dec 13, 2023)
4-6078988-C-T		not specified	Uncertain significance (May 23, 2024)
4-6080183-C-T		not specified	Uncertain significance (Jun 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C4orf50	protein_coding	protein_coding	ENST00000531445	7	32701

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.74e-19	0.00204	123192	21	2535	125748	0.0102

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.123	422	415	1.02	0.0000227	4838
Missense in Polyphen		69	62.886	1.0972		859
Synonymous	-0.979	196	179	1.09	0.0000111	1520
Loss of Function	-0.246	27	25.7	1.05	0.00000109	318

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00825	0.00824
Ashkenazi Jewish	0.00447	0.00437
East Asian	0.00729	0.00720
Finnish	0.0314	0.0312
European (Non-Finnish)	0.0124	0.0122
Middle Eastern	0.00729	0.00720
South Asian	0.00157	0.00150
Other	0.0106	0.0105

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR2: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gm1043