TTC28

tetratricopeptide repeat domain 28, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 22:27978013-28679840

Links

ENSG00000100154 ∙ NCBI:23331 ∙ OMIM:615098 ∙ HGNC:29179 ∙ Uniprot:Q96AY4 ∙ 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 TTC28 gene.

• Inborn genetic diseases (103 variants)
• not provided (24 variants)
• TTC28-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTC28 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				10	7	17
missense			97	8	2	107
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	98	18	9

Variants in TTC28

This is a list of pathogenic ClinVar variants found in the TTC28 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-27982301-C-T		not specified	Likely benign (Jul 19, 2022)
22-27982306-G-A		not specified	Uncertain significance (Nov 23, 2021)
22-27982324-G-A		not specified	Uncertain significance (Aug 12, 2021)
22-27982348-G-A		not specified	Uncertain significance (Jul 13, 2021)
22-27982363-C-T		TTC28-related disorder	Likely benign (Mar 01, 2022)
22-27982396-G-C		TTC28-related disorder	Benign (Jan 03, 2020)
22-27982470-T-C		TTC28-related disorder	Likely benign (Mar 09, 2020)
22-27982532-G-A		not specified	Uncertain significance (Dec 26, 2023)
22-27982536-G-C		not specified	Uncertain significance (Jul 09, 2021)
22-27982636-T-G		not specified	Uncertain significance (Aug 16, 2022)
22-27982669-C-G		not specified	Uncertain significance (Oct 03, 2022)
22-27982673-C-T		not specified	Uncertain significance (Nov 21, 2022)
22-27982797-G-A			Likely benign (Jul 19, 2018)
22-27982851-G-A		TTC28-related disorder	Likely benign (Feb 23, 2019)
22-27982862-G-A		not specified	Uncertain significance (Aug 17, 2021)
22-27982964-G-T		not specified	Uncertain significance (Aug 04, 2022)
22-27983000-T-C		not specified	Uncertain significance (Feb 17, 2024)
22-27983028-C-T			Likely benign (Dec 31, 2019)
22-27983070-C-T		TTC28-related disorder	Benign (Dec 31, 2019)
22-27983071-G-A		not specified	Likely benign (Jun 09, 2022)
22-27983078-C-T		not specified	Likely benign (Jun 28, 2023)
22-27983081-C-T		not specified	Uncertain significance (Nov 30, 2021)
22-27983108-C-A		not specified	Uncertain significance (Jan 03, 2024)
22-27983132-G-A		not specified	Conflicting classifications of pathogenicity (Nov 30, 2021)
22-27983140-G-T		not specified	Uncertain significance (Sep 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTC28	protein_coding	protein_coding	ENST00000397906	23	701850

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	3.43e-9	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.17	925	1.36e+3	0.682	0.0000789	16061
Missense in Polyphen		349	591.58	0.58995		6989
Synonymous	3.71	465	579	0.804	0.0000362	5068
Loss of Function	8.22	10	97.8	0.102	0.00000546	1135

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: During mitosis, may be involved in the condensation of spindle midzone microtubules, leading to the formation of midbody. {ECO:0000269|PubMed:23036704}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• rvis_EVS: 0.89
• rvis_percentile_EVS: 89.3

Haploinsufficiency Scores

• pHI: 0.434
• ghis: 0.452

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.905

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttc28
• Phenotype: craniofacial phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); hematopoietic system phenotype; growth/size/body region phenotype; limbs/digits/tail phenotype; skeleton phenotype

Gene ontology

• Biological process: cell cycle;regulation of mitotic cell cycle;cell division
• Cellular component: spindle pole;cytoplasm;microtubule organizing center;midbody;mitotic spindle
• Molecular function: kinase binding