C11orf42

chromosome 11 open reading frame 42

Basic information

Region (hg38): 11:6205557-6211135

Links

ENSG00000180878 ∙ NCBI:160298 ∙ ∙ HGNC:28541 ∙ Uniprot:Q8N5U0 ∙ 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 C11orf42 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C11orf42 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 C11orf42

This is a list of pathogenic ClinVar variants found in the C11orf42 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-6210329-C-G			Likely benign (Mar 01, 2024)
11-6210475-T-C		not specified	Uncertain significance (Aug 02, 2021)
11-6210514-C-T		not specified	Uncertain significance (Jun 11, 2021)
11-6210556-C-T		not specified	Uncertain significance (Nov 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C11orf42	protein_coding	protein_coding	ENST00000316375	3	5567

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.04e-8	0.206	125665	0	83	125748	0.000330

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0522	195	193	1.01	0.0000112	2089
Missense in Polyphen		60	60.801	0.98682		756
Synonymous	-0.842	92	82.3	1.12	0.00000436	763
Loss of Function	0.298	12	13.2	0.911	9.20e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000296	0.000296
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00266	0.00267
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000134	0.000132
Middle Eastern	0.00266	0.00267
South Asian	0.0000660	0.0000653
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.717
• rvis_EVS: 0
• rvis_percentile_EVS: 53.73

Haploinsufficiency Scores

• pHI: 0.309
• hipred: N
• hipred_score: 0.144
• ghis: 0.415

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: Gm5901