SPHKAP

protein-coding

SPHK1 interactor, AKAP domain containing, the group of A-kinase anchoring proteins

Gene summary

Enables protein kinase A binding activity. Predicted to be located in Z disc. Predicted to be active in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001142644.2

Inheritance

—

ClinVar variants

U:246B:25

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.19

Max pathogenic AF

—

Genomic locus

chr2:227,979,955-228,181,687

External References & Databases

Ensembl (ENSG00000153820)

Transcript & Mutation Effects

hg38 • Region Span ~201.7 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 SPHKAP variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 261

not providedTotal: 11

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001142644.2. 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				3 clinvar		3
missense			241 clinvar	21 clinvar	1 clinvar	263
nonsense			2 clinvar			2
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	246	24	1	271

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001142644.2	RefSeq	NP_001136116.1	12	MANE Select
ENST00000392056.8	Ensembl	ENSP00000375909.3	12	MANE Select
NM_030623.4	RefSeq	NP_085126.2	11	Standard
ENST00000344657.5	Ensembl	ENSP00000339886.5	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

phospholipids as signalling intermediaries

Molecular Function

protein binding
protein kinase A binding

Cellular Component

cytoplasm
mitochondrion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000392056
Coding exons: 12
Length: 201696
Individuals with no LoFs: 125711
Homozygous LoFs: 0
Heterozygous LoFs: 37
Defined: 125748
p: 0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.756	979	915	1.07	0.0000490	11207
Missense (PolyPhen)		252	265.06	0.95073		3427
Synonymous	0.745	351	369	0.951	0.0000223	3322
Loss of Function	5.86	12	61.6	0.195	0.00000325	757

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.00016	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Anchoring protein that binds preferentially to the type I regulatory subunit of c-AMP-dependent protein kinase (PKA type I) and targets it to distinct subcellular compartments. May act as a converging factor linking cAMP and sphingosine signaling pathways. Plays a regulatory role in the modulation of SPHK1. {ECO:0000269|PubMed:12080051, ECO:0000269|PubMed:20394097}.;

Recessive Scores

pRec: 0.0877

Intolerance Scores

LoFtool: 0.575
RVIS EVS: -0.8
RVIS percentile EVS: 12.34

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.133

Gene Damage Prediction

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