TOGARAM2

TOG array regulator of axonemal microtubules 2, the group of TOG domain containing

Basic information

Region (hg38): 2:28956611-29052230

Previous symbols: [ "FAM179A" ]

Links

ENSG00000189350 ∙ NCBI:165186 ∙ ∙ HGNC:33715 ∙ Uniprot:Q6ZUX3 ∙ 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 TOGARAM2 gene.

• not_specified (192 variants)
• not_provided (3 variants)
• Hearing_loss,_autosomal_recessive (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TOGARAM2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000199280.4. 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				2		2
missense			171	20		191
nonsense		1				1
start loss						0
frameshift				1		1
splice donor/acceptor (+/-2bp)						0
Total	0	1	171	23	0

Highest pathogenic variant AF is 6.90639e-7

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TOGARAM2	protein_coding	protein_coding	ENST00000379558	19	104763

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.31e-16	0.147	124346	5	1242	125593	0.00498

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.483	536	568	0.943	0.0000346	6409
Missense in Polyphen		123	128.02	0.96076		1626
Synonymous	-0.267	251	246	1.02	0.0000159	2135
Loss of Function	1.19	29	36.8	0.789	0.00000181	466

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0175	0.0167
Ashkenazi Jewish	0.000499	0.000497
East Asian	0.000447	0.000435
Finnish	0.00781	0.00691
European (Non-Finnish)	0.00652	0.00616
Middle Eastern	0.000447	0.000435
South Asian	0.000863	0.000784
Other	0.00481	0.00458

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 3.2
• rvis_percentile_EVS: 99.33

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Togaram2