C11orf54

chromosome 11 open reading frame 54

Basic information

Region (hg38): 11:93741590-93764749

Links

ENSG00000182919 ∙ NCBI:28970 ∙ OMIM:615810 ∙ HGNC:30204 ∙ Uniprot:Q9H0W9 ∙ 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 C11orf54 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C11orf54 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						0
Total	0	0	1	0	0

Variants in C11orf54

This is a list of pathogenic ClinVar variants found in the C11orf54 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-93759857-C-T		not specified	Uncertain significance (Aug 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C11orf54	protein_coding	protein_coding	ENST00000528288	7	23159

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.87e-8	0.172	125622	0	124	125746	0.000493

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.207	130	137	0.950	0.00000641	1740
Missense in Polyphen		52	52.271	0.99482		610
Synonymous	1.03	38	47.0	0.809	0.00000216	492
Loss of Function	0.193	12	12.7	0.942	6.09e-7	169

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000294	0.000293
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000110	0.000109
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000906	0.000897
Middle Eastern	0.000110	0.000109
South Asian	0.000265	0.000261
Other	0.000168	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Exhibits ester hydrolase activity on the substrate p- nitrophenyl acetate. {ECO:0000269|PubMed:16522806}.

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.410
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.18

Haploinsufficiency Scores

• pHI: 0.0993
• hipred: N
• hipred_score: 0.333
• ghis: 0.448

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• 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: 4931406C07Rik

Gene ontology

• Cellular component: nucleus;nucleoplasm;nuclear body;extracellular exosome
• Molecular function: protein binding;zinc ion binding;hydrolase activity, acting on ester bonds