C1orf53

chromosome 1 open reading frame 53

Basic information

Region (hg38): 1:197902630-197907367

Links

ENSG00000203724 ∙ NCBI:388722 ∙ ∙ HGNC:30003 ∙ Uniprot:Q5VUE5 ∙ 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 C1orf53 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1orf53 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			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	0	0

Variants in C1orf53

This is a list of pathogenic ClinVar variants found in the C1orf53 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-197902678-C-A		not specified	Uncertain significance (Sep 16, 2021)
1-197902726-C-T		not specified	Uncertain significance (Sep 17, 2021)
1-197905811-T-C		not specified	Uncertain significance (Aug 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1orf53	protein_coding	protein_coding	ENST00000367393	3	4721

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000561	0.276	124601	0	37	124638	0.000148

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0806	63	64.8	0.972	0.00000290	883
Missense in Polyphen		17	21.287	0.79861		285
Synonymous	-0.591	33	29.0	1.14	0.00000141	293
Loss of Function	-0.292	6	5.28	1.14	2.27e-7	67

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00196	0.00146
Ashkenazi Jewish	0.00	0.00
East Asian	0.000448	0.000445
Finnish	0.00	0.00
European (Non-Finnish)	0.0000354	0.0000354
Middle Eastern	0.000448	0.000445
South Asian	0.00	0.00
Other	0.000196	0.000165

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.622
• rvis_EVS: 0.19
• rvis_percentile_EVS: 66.57

Haploinsufficiency Scores

• pHI: 0.0695
• hipred: N
• hipred_score: 0.153
• ghis: 0.409

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: 2310009B15Rik