CLIP4

protein-coding

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

Gene summary

Predicted to enable microtubule plus-end binding activity. Predicted to be involved in cytoplasmic microtubule organization. Predicted to be active in cell cortex; microtubule plus-end; and nucleus. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

RSNL2

MANE transcript

NM_024692.6

Inheritance

—

ClinVar variants

U:95B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.53

Max pathogenic AF

—

Genomic locus

chr2:29,097,705-29,199,777

External References & Databases

Ensembl (ENSG00000115295)

Transcript & Mutation Effects

hg38 • Region Span ~102.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CLIP4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 86

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024692.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar		1 clinvar	3
missense			88 clinvar			88
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	95	0	1	96

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 95 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024692.6	RefSeq	NP_078968.3	15	MANE Select
ENST00000320081.10	Ensembl	ENSP00000327009.5	15	MANE Select
NM_001287527.2	RefSeq	NP_001274456.1	15	Standard
NM_001287528.2	RefSeq	NP_001274457.1	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000320081
Coding exons: 15
Length: 91939
Individuals with no LoFs: 125699
Homozygous LoFs: 0
Heterozygous LoFs: 49
Defined: 125748
p: 0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.455	358	383	0.935	0.0000196	4580
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00013	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00038	0.00038	rare
Finnish	0.00028	0.00028	rare
European (Non-Finnish)	0.00020	0.00020	rare
South Asian	0.00020	0.00020	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.103

Intolerance Scores

LoFtool: 0.499
RVIS EVS: -0.2
RVIS percentile EVS: 39.17

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.232

Gene Damage Prediction

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