CXorf58

chromosome X open reading frame 58

Basic information

Region (hg38): X:23908006-23939509

Links

ENSG00000165182 ∙ NCBI:254158 ∙ ∙ HGNC:26356 ∙ Uniprot:Q96LI9 ∙ 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 CXorf58 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CXorf58 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				1		1
missense			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	1	0

Variants in CXorf58

This is a list of pathogenic ClinVar variants found in the CXorf58 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-23916245-A-C		not specified	Uncertain significance (Jun 11, 2021)
X-23927251-G-C		not specified	Uncertain significance (Sep 01, 2021)
X-23935297-T-C			Likely benign (Apr 01, 2022)
X-23935338-G-A		not specified	Uncertain significance (Jun 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CXorf58	protein_coding	protein_coding	ENST00000379211	8	31707

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.07e-7	0.330	123899	575	1084	125558	0.00663

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.404	116	129	0.900	0.0000106	2184
Missense in Polyphen		36	37.647	0.95625		652
Synonymous	-0.108	43	42.1	1.02	0.00000334	609
Loss of Function	0.495	11	12.9	0.851	0.00000116	208

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00533	0.00486
Ashkenazi Jewish	0.0189	0.0125
East Asian	0.00	0.00
Finnish	0.00346	0.00250
European (Non-Finnish)	0.0157	0.0104
Middle Eastern	0.00	0.00
South Asian	0.0102	0.00517
Other	0.0108	0.00721

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.774
• rvis_EVS: 0.73
• rvis_percentile_EVS: 86.17

Haploinsufficiency Scores

• pHI: 0.118
• hipred: N
• hipred_score: 0.146

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	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Fam90a1b