C21orf58

chromosome 21 open reading frame 58

Basic information

Region (hg38): 21:46300181-46323875

Links

ENSG00000160298 ∙ NCBI:54058 ∙ ∙ HGNC:1300 ∙ Uniprot:P58505 ∙ 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 C21orf58 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C21orf58 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	1

Variants in C21orf58

This is a list of pathogenic ClinVar variants found in the C21orf58 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-46302057-G-A		not specified	Uncertain significance (Nov 12, 2021)
21-46302071-A-ATGG		not specified	Benign (Mar 29, 2016)
21-46302115-T-C		not specified	Uncertain significance (Sep 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C21orf58	protein_coding	protein_coding	ENST00000291691	8	23695

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.26e-12	0.0132	125415	0	35	125450	0.000140

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.352	152	165	0.923	0.00000927	1973
Missense in Polyphen		31	30.597	1.0132		370
Synonymous	-1.48	86	70.2	1.23	0.00000402	708
Loss of Function	-0.527	17	14.8	1.15	7.19e-7	160

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000327	0.000307
Ashkenazi Jewish	0.00	0.00
East Asian	0.000391	0.000381
Finnish	0.0000936	0.0000924
European (Non-Finnish)	0.000113	0.0000971
Middle Eastern	0.000391	0.000381
South Asian	0.000198	0.000196
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.6

Haploinsufficiency Scores

• pHI: 0.0846
• hipred: N
• hipred_score: 0.123
• ghis: 0.461

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: 2610028H24Rik