TTC28

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

Basic information

Region (hg38): 22:27978014-28679840

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.

• not_specified (308 variants)
• TTC28-related_disorder (29 variants)
• not_provided (25 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. These statistics are base on transcript: NM_001145418.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				24	10	34
missense			300	14	1	315
nonsense						0
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	301	38	11

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