CATIP

ciliogenesis associated TTC17 interacting protein

Basic information

Region (hg38): 2:218356857-218369962

Previous symbols: [ "C2orf62" ]

Links

ENSG00000158428 ∙ NCBI:375307 ∙ OMIM:619387 ∙ HGNC:25062 ∙ Uniprot:Q7Z7H3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 54	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary	32503832

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CATIP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CATIP 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						0
missense			19	2		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	0

Variants in CATIP

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

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

Position	Type	Phenotype	Significance	ClinVar
2-218357128-C-T		not specified	Uncertain significance (Mar 02, 2023)
2-218357133-T-A		not specified	Likely benign (Dec 03, 2021)
2-218357169-G-A		not specified	Likely benign (Apr 15, 2024)
2-218357172-T-A		Spermatogenic failure 54	Pathogenic (Jun 16, 2021)
2-218357585-C-T		not specified	Uncertain significance (Aug 01, 2024)
2-218357691-C-G		not specified	Uncertain significance (Sep 22, 2023)
2-218357693-G-A		not specified	Uncertain significance (Jan 08, 2024)
2-218357696-G-C		not specified	Uncertain significance (Mar 29, 2023)
2-218357725-T-G		not specified	Uncertain significance (Jul 05, 2023)
2-218357732-T-G		not specified	Uncertain significance (Feb 12, 2024)
2-218360588-A-G		not specified	Uncertain significance (Jan 21, 2022)
2-218360621-G-C		not specified	Uncertain significance (Aug 16, 2021)
2-218364661-C-T		not specified	Uncertain significance (Jun 22, 2023)
2-218364733-T-A		not specified	Uncertain significance (Apr 29, 2024)
2-218367056-C-A		not specified	Uncertain significance (Dec 13, 2023)
2-218367080-T-C		not specified	Uncertain significance (Aug 11, 2022)
2-218367082-C-A		not specified	Uncertain significance (Dec 12, 2023)
2-218367094-G-C		not specified	Uncertain significance (Mar 15, 2024)
2-218367436-T-C		not specified	Uncertain significance (Aug 20, 2023)
2-218367483-G-A		not specified	Uncertain significance (May 11, 2022)
2-218367747-G-C			Likely benign (Oct 01, 2022)
2-218367842-G-A		not specified	Uncertain significance (May 26, 2022)
2-218367846-A-T		not specified	Uncertain significance (Aug 16, 2021)
2-218367887-G-A		not specified	Uncertain significance (Aug 01, 2024)
2-218367894-G-A		not specified	Uncertain significance (May 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CATIP	protein_coding	protein_coding	ENST00000289388	10	11244

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.08e-9	0.432	125714	0	34	125748	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.317	215	228	0.941	0.0000119	2514
Missense in Polyphen		67	76.477	0.87608		840
Synonymous	0.0139	95	95.2	0.998	0.00000508	762
Loss of Function	0.993	16	20.9	0.766	0.00000107	235

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000388	0.000387
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.000163	0.000163
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in primary ciliogenesis by modulating actin polymerization. {ECO:0000269|PubMed:24475127}.

Intolerance Scores

• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.72

Haploinsufficiency Scores

• pHI: 0.181
• hipred: N
• hipred_score: 0.172
• ghis: 0.470

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Catip
• Phenotype: immune system phenotype; reproductive system phenotype; hematopoietic system phenotype

Zebrafish Information Network

• Gene name: catip
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: actin filament polymerization;cilium organization
• Cellular component: nucleus;cytoplasm;plasma membrane;actin cytoskeleton
• Molecular function: protein binding