SPHKAP

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

Basic information

Region (hg38): 2:227979955-228181687

Links

ENSG00000153820 ∙ NCBI:80309 ∙ OMIM:611646 ∙ HGNC:30619 ∙ Uniprot:Q2M3C7 ∙ 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 SPHKAP gene.

• not_specified (230 variants)
• not_provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPHKAP gene is commonly pathogenic or not. These statistics are base on transcript: NM_001142644.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3		3
missense			210	20	1	231
nonsense			1			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	211	23	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPHKAP	protein_coding	protein_coding	ENST00000392056	12	201696

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.936	0.0641	125711	0	37	125748	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.756	979	915	1.07	0.0000490	11207
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000425	0.000423
Ashkenazi Jewish	0.000300	0.000298
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.0000544	0.0000544
South Asian	0.000165	0.000163
Other	0.00	0.00

dbNSFP

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}.
• Pathway: phospholipids as signalling intermediaries (Consensus)

Recessive Scores

• pRec: 0.0877

Intolerance Scores

• loftool: 0.575
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.34

Haploinsufficiency Scores

• pHI: 0.176
• hipred: N
• hipred_score: 0.445
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.133

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sphkap

Gene ontology

• Cellular component: cytoplasm;mitochondrion
• Molecular function: protein binding;protein kinase A binding