CSTPP1

centriolar satellite-associated tubulin polyglutamylase complex regulator 1

Basic information

Region (hg38): 11:46936688-47164385

Previous symbols: [ "C11orf49" ]

Links

ENSG00000149179 ∙ NCBI:79096 ∙ ∙ HGNC:28720 ∙ Uniprot:Q9H6J7 ∙ 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 CSTPP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSTPP1 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
missense			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	1	0

Variants in CSTPP1

This is a list of pathogenic ClinVar variants found in the CSTPP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-46987214-G-A		not specified	Uncertain significance (Nov 08, 2021)
11-47161147-G-C		not specified	Uncertain significance (Jun 22, 2021)
11-47161623-C-T			Likely benign (Apr 01, 2023)
11-47161624-G-A		not specified	Uncertain significance (Sep 17, 2021)
11-47164209-C-T		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSTPP1	protein_coding	protein_coding	ENST00000378615	9	227697

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.24e-11	0.132	125548	0	200	125748	0.000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.123	193	198	0.975	0.0000113	2189
Missense in Polyphen		81	74.122	1.0928		814
Synonymous	-1.03	93	81.2	1.15	0.00000478	665
Loss of Function	0.563	18	20.8	0.867	0.00000130	211

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00195	0.00195
Ashkenazi Jewish	0.000299	0.000298
East Asian	0.00169	0.00169
Finnish	0.000556	0.000554
European (Non-Finnish)	0.000627	0.000624
Middle Eastern	0.00169	0.00169
South Asian	0.000947	0.000948
Other	0.00114	0.00114

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.790
• rvis_EVS: -0.53
• rvis_percentile_EVS: 20.78

Haploinsufficiency Scores

• pHI: 0.251
• hipred: N
• hipred_score: 0.216
• ghis: 0.637

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: 1110051M20Rik

Gene ontology

• Molecular function: protein binding