SPHKAP

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

Basic information

Region (hg38): 2:227979954-228181687

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.

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.

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				2		2
missense			94	13	2	109
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	94	15	3

Variants in SPHKAP

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

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

Position	Type	Phenotype	Significance	ClinVar
2-227981754-C-T		not specified	Uncertain significance (Apr 20, 2024)
2-227981770-C-T		not specified	Uncertain significance (Oct 18, 2021)
2-227981832-C-T		not specified	Likely benign (Dec 01, 2022)
2-227981848-C-G			Benign (Jan 24, 2018)
2-227981851-C-A		not specified	Uncertain significance (Mar 08, 2024)
2-227991043-G-T		not specified	Uncertain significance (Oct 05, 2023)
2-227991049-C-A		not specified	Uncertain significance (Aug 11, 2021)
2-227991053-G-C		not specified	Uncertain significance (Mar 28, 2024)
2-227991070-C-T			Uncertain significance (Feb 08, 2023)
2-227991116-G-C		not specified	Uncertain significance (Jan 23, 2024)
2-227991277-C-T			Benign (Dec 31, 2019)
2-227993525-G-T			Benign (Mar 29, 2018)
2-227993549-G-T		not specified	Uncertain significance (Aug 12, 2021)
2-227993600-G-A		not specified	Uncertain significance (Sep 16, 2021)
2-227995618-G-T		not specified	Uncertain significance (Mar 22, 2023)
2-227995626-G-C		not specified	Uncertain significance (Jun 10, 2024)
2-227995627-C-T		not specified	Uncertain significance (Jan 24, 2024)
2-227995689-C-T		not specified	Uncertain significance (Jul 06, 2022)
2-228016409-T-C		not specified	Uncertain significance (Sep 14, 2022)
2-228016414-T-G		not specified	Uncertain significance (Jun 05, 2024)
2-228016506-T-C		not specified	Uncertain significance (Jan 24, 2023)
2-228016534-A-C			Likely benign (Aug 01, 2022)
2-228016586-G-A		not specified	Uncertain significance (Jul 19, 2023)
2-228016598-C-T		not specified	Uncertain significance (Apr 04, 2024)
2-228016602-T-C		not specified	Uncertain significance (Feb 28, 2023)

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