TTC16

Gene

tetratricopeptide repeat domain 16, the group of Tetratricopeptide repeat domain containing

Gene summary

No gene description available in the current model. Review primary literature for detailed gene function and characteristics.

MANE transcript

NM_144965.3

Inheritance

—

ClinVar variants

U:150B:20

Top phenotype

Premature ovarian insufficiency

gnomAD constraint

pLI —, LoF o/e 0.85

Max pathogenic AF

—

Genomic locus

chr9:127,716,079-127,731,590

External References & Databases

Ensembl (ENSG00000167094)

Transcript & Mutation Effects

hg38 • Region Span ~15.5 kb

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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 TTC16 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 163

not providedTotal: 3

Premature ovarian insufficiencyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_144965.3. 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				3 clinvar		3
missense			148 clinvar	17 clinvar		165
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	150	20	0	170

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_144965.3	RefSeq	NP_659402.1	14	MANE Select
ENST00000373289.4	Ensembl	ENSP00000362386.3	14	MANE Select
NM_001317037.2	RefSeq	NP_001303966.1	14	Standard
ENST00000862124.1	Ensembl	ENSP00000532183.1	13	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373289
Coding exons: 14
Length: 15535
Individuals with no LoFs: 125401
Homozygous LoFs: 0
Heterozygous LoFs: 343
Defined: 125744
p: 0.00136

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.431	477	504	0.946	0.0000297	5674
Missense (PolyPhen)		138	133.79	1.0315		1450
Synonymous	0.911	198	215	0.921	0.0000130	1705
Loss of Function	0.855	30	35.5	0.845	0.00000174	390

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0021	0.0021	notable
Latino/Admixed American	0.0036	0.0035	notable
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.0037	0.0036	notable
Finnish	0.000048	0.000046	rare
European (Non-Finnish)	0.00061	0.00056	rare
South Asian	0.0016	0.0016	notable
Other	0.0010	0.00098	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.980
RVIS EVS: 0.65
RVIS percentile EVS: 84.18

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.277

Gene Damage Prediction

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