TSKU

tsukushi, small leucine rich proteoglycan

Basic information

Region (hg38): 11:76782251-76798153

Previous symbols: [ "LRRC54" ]

Links

ENSG00000182704 ∙ NCBI:25987 ∙ OMIM:608015 ∙ HGNC:28850 ∙ Uniprot:Q8WUA8 ∙ 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 TSKU gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSKU 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				1	1	2
missense			31	2		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	3	1

Variants in TSKU

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

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

Position	Type	Phenotype	Significance	ClinVar
11-76795646-C-T			Benign (Nov 01, 2022)
11-76795647-G-A		not specified	Uncertain significance (Aug 02, 2021)
11-76795647-G-C		not specified	Uncertain significance (Jul 09, 2021)
11-76795767-A-T		not specified	Uncertain significance (Feb 28, 2023)
11-76795774-C-T		not specified	Uncertain significance (Dec 07, 2021)
11-76795858-C-G		not specified	Uncertain significance (Jun 29, 2022)
11-76795867-C-T		not specified	Uncertain significance (May 24, 2024)
11-76795924-C-A		not specified	Uncertain significance (Apr 06, 2023)
11-76795924-C-T		not specified	Uncertain significance (Dec 11, 2023)
11-76795939-G-A		not specified	Uncertain significance (Sep 20, 2023)
11-76795951-C-T		not specified	Uncertain significance (Jun 30, 2022)
11-76795980-G-A		not specified	Uncertain significance (Dec 13, 2022)
11-76795992-G-A		not specified	Uncertain significance (May 21, 2024)
11-76796019-G-A		not specified	Uncertain significance (Dec 21, 2022)
11-76796046-C-T		not specified	Uncertain significance (Jun 09, 2022)
11-76796074-C-T		not specified	Uncertain significance (Apr 18, 2023)
11-76796098-A-C		not specified	Uncertain significance (Dec 17, 2021)
11-76796100-G-T			Likely benign (Jun 16, 2021)
11-76796113-A-C		not specified	Uncertain significance (Feb 06, 2023)
11-76796128-G-A		not specified	Uncertain significance (Sep 29, 2022)
11-76796146-C-T		not specified	Uncertain significance (Feb 14, 2023)
11-76796164-C-T		not specified	Uncertain significance (Oct 25, 2022)
11-76796211-G-A		not specified	Uncertain significance (Aug 14, 2023)
11-76796287-C-A		not specified	Uncertain significance (Nov 22, 2021)
11-76796287-C-T		not specified	Uncertain significance (Nov 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSKU	protein_coding	protein_coding	ENST00000527881	1	15904

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.854	0.144	125715	0	3	125718	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.605	192	217	0.885	0.0000153	2214
Missense in Polyphen		63	82.566	0.76303		972
Synonymous	-1.18	122	106	1.15	0.00000748	845
Loss of Function	2.33	0	6.32	0.00	3.58e-7	59

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000881	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Ectoderm Differentiation (Consensus)

Recessive Scores

• pRec: 0.403

Intolerance Scores

• loftool: 0.274
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.96

Haploinsufficiency Scores

• pHI: 0.248
• hipred: N
• hipred_score: 0.366
• ghis: 0.446

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.185

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tsku
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of gene expression;corpus callosum morphogenesis;lateral ventricle development;anterior commissure morphogenesis;negative regulation of Wnt signaling pathway;ciliary body morphogenesis
• Cellular component: extracellular space