C11orf65

chromosome 11 open reading frame 65

Basic information

Region (hg38): 11:108308519-108467531

Links

ENSG00000166323 ∙ NCBI:160140 ∙ ∙ HGNC:28519 ∙ Uniprot:Q8NCR3 ∙ 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 C11orf65 gene.

• Ataxia-telangiectasia syndrome (226 variants)
• Hereditary cancer-predisposing syndrome (154 variants)
• Familial cancer of breast (151 variants)
• not provided (39 variants)
• Familial cancer of breast;Ataxia-telangiectasia syndrome (8 variants)
• Ataxia-telangiectasia syndrome;Familial cancer of breast (6 variants)
• ATM-related disorder (6 variants)
• Gastric cancer (6 variants)
• Breast and/or ovarian cancer (4 variants)
• ATM-related cancer predisposition (4 variants)
• Malignant tumor of urinary bladder (3 variants)
• Malignant tumor of breast (3 variants)
• Tip-toe gait (2 variants)
• Abnormal central motor function (1 variants)
• Ataxia-telangiectasia without immunodeficiency (1 variants)
• not specified (1 variants)
• Ataxia-telangiectasia syndrome;Malignant tumor of breast (1 variants)
• Colorectal cancer (1 variants)
• Breast cancer, susceptibility to (1 variants)
• Familial ovarian cancer (1 variants)
• Hereditary breast ovarian cancer syndrome (1 variants)
• Malignant glioma (1 variants)
• Breast carcinoma (1 variants)
• Ataxia-telangiectasia syndrome;Breast cancer, susceptibility to (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C11orf65 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				2		2
splice region				5		5
non coding	342	270	1496	875	91	3074
Total	342	270	1498	877	91

Highest pathogenic variant AF is 0.0000329

Variants in C11orf65

This is a list of pathogenic ClinVar variants found in the C11orf65 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-108309009-T-C			Benign/Likely benign (Nov 01, 2024)
11-108309080-A-G		Ataxia-telangiectasia syndrome	Uncertain significance (Nov 10, 2022)
11-108309104-G-A		Familial cancer of breast • Hereditary cancer-predisposing syndrome • Ataxia-telangiectasia syndrome • ATM-related disorder	Conflicting classifications of pathogenicity (Dec 12, 2024)
11-108309104-G-C		Ataxia-telangiectasia syndrome	Likely benign (Aug 20, 2024)
11-108309104-G-T		Ataxia-telangiectasia syndrome	Likely benign (Apr 10, 2024)
11-108309105-G-C		ATM-related disorder	Likely benign (Dec 13, 2019)
11-108309108-AAAGACATGCATTC-A		Ataxia-telangiectasia syndrome	Likely benign (Jan 18, 2023)
11-108309110-A-G		Ataxia - telangiectasia variant • Hereditary cancer-predisposing syndrome • Breast and/or ovarian cancer • Ataxia-telangiectasia syndrome • Familial cancer of breast • ATM-related cancer predisposition • Familial cancer of breast;Ataxia-telangiectasia syndrome • ATM-related disorder	Pathogenic (Nov 26, 2024)
11-108309114-A-G		ATM-related disorder	Likely benign (Feb 14, 2024)
11-108309858-A-G		Hereditary cancer-predisposing syndrome	Likely benign (Dec 01, 2015)
11-108310137-CATT-C		Hereditary cancer-predisposing syndrome • Ataxia-telangiectasia syndrome • Familial cancer of breast	Likely benign (Jul 09, 2024)
11-108310139-TTA-T		not specified • Hereditary cancer-predisposing syndrome • Ataxia-telangiectasia syndrome • Familial cancer of breast	Likely benign (Jul 03, 2024)
11-108310140-T-C		Familial cancer of breast	Likely benign (May 24, 2024)
11-108310140-T-G		Ataxia-telangiectasia syndrome	Likely benign (Dec 05, 2023)
11-108310140-TATATCTCATTTTTCTTTAGACCTTCTTC-T		Hereditary cancer-predisposing syndrome	Likely pathogenic (Jul 21, 2023)
11-108310141-A-G		Hereditary cancer-predisposing syndrome • Ataxia-telangiectasia syndrome • Familial cancer of breast	Likely benign (Jul 19, 2024)
11-108310143-ATC-A		not specified • Ataxia-telangiectasia syndrome	Likely benign (May 25, 2021)
11-108310145-C-G		Ataxia-telangiectasia syndrome	Likely benign (Sep 27, 2023)
11-108310146-T-A		Ataxia-telangiectasia syndrome	Likely benign (Jan 20, 2025)
11-108310147-C-G		Hereditary cancer-predisposing syndrome	Uncertain significance (Sep 28, 2020)
11-108310147-C-T		not specified • Hereditary cancer-predisposing syndrome • Ataxia-telangiectasia syndrome • Familial cancer of breast	Likely benign (Jul 18, 2024)
11-108310148-A-G		not specified • Familial cancer of breast • Ataxia-telangiectasia syndrome	Likely benign (May 24, 2024)
11-108310148-AT-A		Familial cancer of breast	Likely benign (May 24, 2024)
11-108310149-T-C		not specified • Ataxia-telangiectasia syndrome • Familial cancer of breast	Likely benign (Oct 21, 2024)
11-108310152-T-C		Familial cancer of breast	Likely benign (May 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C11orf65	protein_coding	protein_coding	ENST00000393084	8	159013

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.02e-14	0.00431	125497	0	248	125745	0.000987

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.370	148	161	0.918	0.00000748	2085
Missense in Polyphen		40	45.264	0.88371		577
Synonymous	0.904	43	51.2	0.839	0.00000235	535
Loss of Function	-0.804	19	15.6	1.22	7.38e-7	194

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00106	0.00105
Ashkenazi Jewish	0.00	0.00
East Asian	0.000115	0.000109
Finnish	0.000279	0.000277
European (Non-Finnish)	0.00173	0.00172
Middle Eastern	0.000115	0.000109
South Asian	0.000596	0.000588
Other	0.000496	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0950

Intolerance Scores

• loftool: 0.632
• rvis_EVS: 0.66
• rvis_percentile_EVS: 84.44

Haploinsufficiency Scores

• pHI: 0.103
• hipred: N
• hipred_score: 0.123

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: 4930550C14Rik

Zebrafish Information Network

• Gene name: gb:co360592
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: curved

Gene ontology

• Molecular function: protein binding