CASKIN1

protein-coding

CASK interacting protein 1, the group of Ankyrin repeat domain containing|Sterile alpha motif domain containing

Gene summary

Enables identical protein binding activity. Predicted to be involved in regulation of postsynaptic density assembly and signal transduction. Predicted to be located in cytoplasm. Predicted to be active in glutamatergic synapse. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_020764.4

Inheritance

—

ClinVar variants

U:297B:13

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.06

Max pathogenic AF

—

Genomic locus

chr16:2,177,180-2,196,605

External References & Databases

Ensembl (ENSG00000167971)

Transcript & Mutation Effects

hg38 • Region Span ~19.4 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 CASKIN1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 297

not providedTotal: 10

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020764.4. 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	5 clinvar		7
missense			293 clinvar	8 clinvar		301
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	297	13	0	310

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020764.4	RefSeq	NP_065815.1	20	MANE Select
ENST00000343516.8	Ensembl	ENSP00000345436.6	20	MANE Select
ENST00001132584.1	Ensembl	ENSP00000808194.1	20	Standard
XM_024450361.2	RefSeq	XP_024306129.1	18	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

signal transduction

Molecular Function

protein binding
identical protein binding

Cellular Component

cytoplasm
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000343516
Coding exons: 20
Length: 19343
Individuals with no LoFs: 124596
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 124604
p: 0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.79	665	808	0.823	0.0000557	8895
Missense (PolyPhen)		231	350.88	0.65835		3558
Synonymous	-2.53	455	391	1.16	0.0000316	3156
Loss of Function	5.98	3	47.4	0.0633	0.00000265	550

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000030	0.000029	rare
Ashkenazi Jewish	0.00010	0.00010	rare
East Asian	0.000056	0.000056	rare
Finnish	0.000064	0.000046	rare
European (Non-Finnish)	0.000029	0.000027	rare
South Asian	0	0.0	absent
Other	0.00018	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May link the scaffolding protein CASK to downstream intracellular effectors. {ECO:0000250}.;

Recessive Scores

pRec: 0.113

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.811

Gene Damage Prediction

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