CLIP4

CAP-Gly domain containing linker protein family member 4, the group of Ankyrin repeat domain containing

Basic information

Region (hg38): 2:29097704-29199777

Previous symbols: [ "RSNL2" ]

Links

ENSG00000115295 ∙ NCBI:79745 ∙ ∙ HGNC:26108 ∙ Uniprot:Q8N3C7 ∙ 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 CLIP4 gene.

• Neuroblastoma, susceptibility to, 3 (668 variants)
• Hereditary cancer-predisposing syndrome (370 variants)
• not provided (68 variants)
• Inborn genetic diseases (27 variants)
• not specified (21 variants)
• Squamous cell lung carcinoma (5 variants)
• ALK-related condition (5 variants)
• Ovarian cancer (5 variants)
• Neuroblastoma Susceptibility (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLIP4 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			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding		1	512	234	24	771
Total	0	1	538	234	25

Highest pathogenic variant AF is 0.0000131

Variants in CLIP4

This is a list of pathogenic ClinVar variants found in the CLIP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-29121444-G-A		not specified	Uncertain significance (Jan 09, 2024)
2-29121479-G-A		not specified	Uncertain significance (Jan 23, 2023)
2-29131378-T-C		not specified	Uncertain significance (Mar 07, 2023)
2-29132177-A-G		not specified	Uncertain significance (Dec 16, 2022)
2-29133684-A-G		not specified	Uncertain significance (Oct 04, 2022)
2-29133703-G-A		not specified	Uncertain significance (Oct 26, 2022)
2-29133786-A-G		not specified	Uncertain significance (Feb 21, 2024)
2-29133805-C-T		not specified	Uncertain significance (Oct 22, 2021)
2-29133813-A-G		not specified	Uncertain significance (May 15, 2023)
2-29135638-T-G		not specified	Uncertain significance (Aug 02, 2022)
2-29143758-T-C		not specified	Uncertain significance (Jun 13, 2023)
2-29143778-G-A		not specified	Uncertain significance (Jun 05, 2023)
2-29143781-G-A		not specified	Uncertain significance (Apr 25, 2022)
2-29143807-G-C		not specified	Uncertain significance (Feb 15, 2023)
2-29143938-G-A		not specified	Uncertain significance (Jun 06, 2023)
2-29145337-G-A		not specified	Uncertain significance (May 27, 2022)
2-29145363-G-T		not specified	Uncertain significance (Aug 09, 2021)
2-29152711-A-C		not specified	Uncertain significance (May 24, 2023)
2-29152736-A-C		not specified	Uncertain significance (Nov 17, 2022)
2-29152745-A-G		not specified	Uncertain significance (Feb 23, 2023)
2-29157213-T-C		not specified	Uncertain significance (Oct 12, 2021)
2-29160350-A-G		not specified	Uncertain significance (Dec 26, 2023)
2-29160359-G-A		not specified	Uncertain significance (Jun 23, 2021)
2-29160376-C-G		not specified	Uncertain significance (Jan 18, 2023)
2-29163838-G-T		not specified	Uncertain significance (Oct 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLIP4	protein_coding	protein_coding	ENST00000320081	15	91939

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.90e-8	0.993	125699	0	49	125748	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.455	358	383	0.935	0.0000196	4580
Missense in Polyphen		121	134.37	0.90051		1572
Synonymous	0.826	124	136	0.910	0.00000720	1384
Loss of Function	2.46	17	32.0	0.531	0.00000150	425

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000257	0.000257
Ashkenazi Jewish	0.00	0.00
East Asian	0.000382	0.000381
Finnish	0.000279	0.000277
European (Non-Finnish)	0.000205	0.000202
Middle Eastern	0.000382	0.000381
South Asian	0.000196	0.000196
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.499
• rvis_EVS: -0.2
• rvis_percentile_EVS: 39.17

Haploinsufficiency Scores

• pHI: 0.171
• hipred: Y
• hipred_score: 0.557
• ghis: 0.503

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.232

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clip4

Gene ontology

• Cellular component: intracellular membrane-bounded organelle
• Molecular function: protein binding