GPKOW

G-patch domain and KOW motifs, the group of Spliceosomal Bact complex|Spliceosomal P complex|NTC associated proteins|Spliceosomal C complex|G-patch domain containing

Basic information

Region (hg38): X:49113407-49123735

Links

ENSG00000068394 ∙ NCBI:27238 ∙ OMIM:301003 ∙ HGNC:30677 ∙ Uniprot:Q92917 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• holoprosencephaly-hypokinesia-congenital contractures syndrome (Limited), mode of inheritance: XL

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GPKOW gene.

• not_specified (47 variants)
• not_provided (12 variants)
• GPKOW-related_disorder (6 variants)
• Holoprosencephaly-hypokinesia-congenital_contractures_syndrome (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPKOW gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015698.6. 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			1	2	2	5
missense			47	6	1	54
nonsense			1			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	49	8	3

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPKOW	protein_coding	protein_coding	ENST00000156109	11	9818

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00447	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.921	166	203	0.818	0.0000169	3055
Missense in Polyphen		41	59.273	0.69171		922
Synonymous	-0.228	79	76.5	1.03	0.00000584	999
Loss of Function	3.71	0	16.0	0.00	0.00000123	271

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding protein involved in pre-mRNA splicing. {ECO:0000269|PubMed:25296192}.
• Pathway: Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.0872

Intolerance Scores

• loftool: 0.0403
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.69

Haploinsufficiency Scores

• pHI: 0.0738
• hipred: Y
• hipred_score: 0.666
• ghis: 0.490

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpkow

Gene ontology

• Biological process: mRNA splicing, via spliceosome
• Cellular component: nucleus;nucleoplasm;spliceosomal complex
• Molecular function: RNA binding;protein binding