C11orf40

chromosome 11 putative open reading frame 40

Basic information

Region (hg38): 11:4571423-4577820

Links

ENSG00000171987 ∙ NCBI:143501 ∙ ∙ HGNC:23986 ∙ Uniprot:Q8WZ69 ∙ 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 C11orf40 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C11orf40 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	3	0	0

Variants in C11orf40

This is a list of pathogenic ClinVar variants found in the C11orf40 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-4571505-A-T		not specified	Uncertain significance (Jun 21, 2021)
11-4573424-C-T		not specified	Uncertain significance (Oct 27, 2021)
11-4573443-G-C		not specified	Uncertain significance (Sep 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C11orf40	protein_coding	protein_coding	ENST00000307616	4	6398

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000106	0.108	123667	65	1992	125724	0.00821

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.86	203	116	1.75	0.00000567	1414
Missense in Polyphen		12	6.9706	1.7215		74
Synonymous	-3.16	68	41.9	1.62	0.00000207	415
Loss of Function	-0.755	8	6.00	1.33	2.52e-7	79

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0966	0.0972
Ashkenazi Jewish	0.00258	0.00258
East Asian	0.0204	0.0205
Finnish	0.00	0.00
European (Non-Finnish)	0.000336	0.000325
Middle Eastern	0.0204	0.0205
South Asian	0.000753	0.000752
Other	0.00311	0.00310

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.927
• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.49

Haploinsufficiency Scores

• pHI: 0.0822
• 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