C1QTNF5

C1q and TNF related 5, the group of C1q and TNF related

Basic information

Region (hg38): 11:119338941-119340940

Links

ENSG00000223953 ∙ NCBI:114902 ∙ OMIM:608752 ∙ HGNC:14344 ∙ Uniprot:Q9BXJ0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• late-onset retinal degeneration (Strong), mode of inheritance: AD
• late-onset retinal degeneration (Supportive), mode of inheritance: AD
• late-onset retinal degeneration (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Late-onset retinal degeneration	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	12944416; 22277927; 23289492

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the C1QTNF5 gene.

• not provided (136 variants)
• Late-onset retinal degeneration (31 variants)
• Isolated microphthalmia 5 (27 variants)
• Retinal degeneration (17 variants)
• Retinal dystrophy (7 variants)
• Inborn genetic diseases (3 variants)
• Isolated microphthalmia 6 (3 variants)
• not specified (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1QTNF5 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			4	33	1	38
missense	1	3	73			77
nonsense						0
start loss						0
frameshift			2		1	3
inframe indel			2	1		3
splice donor/acceptor (+/-2bp)						0
splice region			4	3		7
non coding			12	13	1	26
Total	1	3	93	47	3

Variants in C1QTNF5

This is a list of pathogenic ClinVar variants found in the C1QTNF5 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-119338986-C-A		Late-onset retinal degeneration • Isolated microphthalmia 5	Uncertain significance (Jan 13, 2018)
11-119339080-G-A		Retinal degeneration • Isolated microphthalmia 5 • Late-onset retinal degeneration	Uncertain significance (Jan 12, 2018)
11-119339095-G-A		Late-onset retinal degeneration • Isolated microphthalmia 5	Uncertain significance (Jan 13, 2018)
11-119339120-G-T		Late-onset retinal degeneration • Isolated microphthalmia 5	Uncertain significance (Jan 13, 2018)
11-119339173-G-T		Retinal degeneration • Late-onset retinal degeneration • Isolated microphthalmia 5	Uncertain significance (Jan 13, 2018)
11-119339269-T-A		Retinal degeneration • Isolated microphthalmia 6	Likely benign (Jun 14, 2016)
11-119339297-G-C		Retinal degeneration • Isolated microphthalmia 5 • Late-onset retinal degeneration	Benign/Likely benign (Jan 12, 2018)
11-119339330-A-G		Late-onset retinal degeneration • Isolated microphthalmia 5	Uncertain significance (Jan 13, 2018)
11-119339349-G-A			Likely benign (Nov 25, 2022)
11-119339352-G-A			Likely benign (Dec 11, 2023)
11-119339360-C-A			Uncertain significance (Apr 23, 2021)
11-119339378-C-T			Uncertain significance (Nov 29, 2022)
11-119339388-GCTGT-G			Uncertain significance (Sep 11, 2023)
11-119339410-T-A			Uncertain significance (Oct 13, 2023)
11-119339415-G-A		C1QTNF5-related disorder	Likely benign (May 10, 2023)
11-119339419-A-G		Isolated microphthalmia 5 • Retinal degeneration • Late-onset retinal degeneration	Uncertain significance (Feb 18, 2022)
11-119339421-G-A			Likely benign (Aug 15, 2022)
11-119339428-C-G			Uncertain significance (Jul 19, 2022)
11-119339433-A-G			Likely benign (Nov 19, 2022)
11-119339434-C-T			Uncertain significance (Sep 20, 2022)
11-119339435-C-G		Retinal dystrophy	Uncertain significance (Jul 17, 2018)
11-119339438-C-T			Uncertain significance (Sep 17, 2021)
11-119339450-C-G		Late-onset retinal degeneration	Likely benign (Mar 25, 2024)
11-119339462-G-A			Uncertain significance (Sep 23, 2022)
11-119339464-T-C			Uncertain significance (Sep 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1QTNF5	protein_coding	protein_coding	ENST00000445041	2	7732

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.836	0.161	124239	0	179	124418	0.000720

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	96	134	0.718	0.00000664	1524
Missense in Polyphen		37	64.153	0.57675		753
Synonymous	0.374	59	62.8	0.940	0.00000357	545
Loss of Function	2.26	0	5.95	0.00	2.55e-7	69

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00475	0.00473
Ashkenazi Jewish	0.000301	0.000298
East Asian	0.000599	0.000598
Finnish	0.0000470	0.0000462
European (Non-Finnish)	0.000590	0.000585
Middle Eastern	0.000599	0.000598
South Asian	0.000327	0.000327
Other	0.000986	0.000982

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Late-onset retinal degeneration (LORD) [MIM:605670]: Autosomal dominant disorder characterized by onset in the fifth to sixth decade with night blindness and punctate yellow-white deposits in the retinal fundus, progressing to severe central and peripheral degeneration, with choroidal neovascularization and chorioretinal atrophy. {ECO:0000269|PubMed:12944416, ECO:0000269|PubMed:22892318}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Haploinsufficiency Scores

• pHI: 0.106
• hipred: Y
• hipred_score: 0.696

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: C1qtnf5
• Phenotype: endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; pigmentation phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); normal phenotype; vision/eye phenotype; hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: protein secretion;inner ear development;protein trimerization
• Cellular component: collagen trimer;extracellular space;plasma membrane;bicellular tight junction;apical plasma membrane;lateral plasma membrane;transport vesicle;cell projection
• Molecular function: identical protein binding