TTC22

protein-coding

tetratricopeptide repeat domain 22, the group of Tetratricopeptide repeat domain containing

Gene summary

This gene encodes a protein with seven tetratricopeptide (TPR) repeats. Tetratricopeptide repeat containing motifs are found in a variety of proteins and may mediate protein-protein interactions and chaperone activity. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jun 2011]

MANE transcript

NM_001114108.2

Inheritance

—

ClinVar variants

U:69B:5

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.62

Max pathogenic AF

—

Genomic locus

chr1:54,779,712-54,801,323

External References & Databases

Ensembl (ENSG00000006555)

Transcript & Mutation Effects

hg38 • Region Span ~21.6 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TTC22 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 69

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001114108.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			67 clinvar	4 clinvar		71
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	69	5	0	74

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001114108.2	RefSeq	NP_001107580.1	7	MANE Select
ENST00000371276.9	Ensembl	ENSP00000360323.4	7	MANE Select
NM_017904.4	RefSeq	NP_060374.2	6	Standard
ENST00000371274.8	Ensembl	ENSP00000360321.4	6	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000371276
Coding exons: 7
Length: 21556
Individuals with no LoFs: 125629
Homozygous LoFs: 0
Heterozygous LoFs: 117
Defined: 125746
p: 0.000465

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.10	239	292	0.819	0.0000177	3550
Missense (PolyPhen)		62	70.443	0.88015		922
Synonymous	2.17	100	132	0.760	0.00000868	1164
Loss of Function	1.54	12	19.3	0.621	0.00000101	234

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00014	0.00012	rare
Latino/Admixed American	0.00032	0.00032	rare
Ashkenazi Jewish	0.00011	0.000099	rare
East Asian	0.00034	0.00033	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00013	0.00012	rare
South Asian	0.0027	0.0027	notable
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.108

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.694

Gene Damage Prediction

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