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.

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.

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			1	1	1	3
missense			29	4		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	30	5	1

Variants in GPKOW

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

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

Position	Type	Phenotype	Significance	ClinVar
X-49113711-C-G		not specified	Uncertain significance (Mar 31, 2024)
X-49113717-C-T		GPKOW-related disorder	Benign (Dec 03, 2019)
X-49113725-G-A		GPKOW-related disorder • not specified	Uncertain significance (Feb 05, 2024)
X-49113759-G-A		GPKOW-related disorder	Benign (Dec 03, 2019)
X-49113867-G-C		not specified	Uncertain significance (Feb 01, 2025)
X-49113870-C-G		Holoprosencephaly-hypokinesia-congenital contractures syndrome	Uncertain significance (Apr 29, 2019)
X-49113905-G-A			Uncertain significance (Sep 29, 2023)
X-49113942-T-C			Likely benign (Jul 13, 2023)
X-49115746-T-G		not specified	Uncertain significance (Jan 26, 2022)
X-49115752-C-T		not specified	Uncertain significance (Feb 08, 2023)
X-49115764-G-A		not specified	Conflicting classifications of pathogenicity (Mar 24, 2023)
X-49115765-T-C		not specified	Uncertain significance (May 23, 2024)
X-49115792-T-C		not specified	Uncertain significance (Jan 24, 2025)
X-49115943-C-T		not specified	Uncertain significance (Jul 26, 2022)
X-49115948-G-T		not specified	Uncertain significance (Jan 23, 2023)
X-49115998-C-G		not specified	Uncertain significance (Nov 23, 2021)
X-49116221-C-T			Likely benign (Dec 01, 2022)
X-49116225-C-A		not specified	Uncertain significance (Jan 23, 2024)
X-49116302-G-A		not specified	Uncertain significance (Nov 10, 2024)
X-49117036-C-T		not specified	Uncertain significance (May 05, 2023)
X-49117080-T-C			Likely benign (Dec 31, 2019)
X-49117105-G-A		not specified	Uncertain significance (Mar 24, 2023)
X-49117116-G-A		not specified	Uncertain significance (Aug 20, 2023)
X-49117123-G-A		not specified	Uncertain significance (Jan 08, 2025)
X-49117614-G-A			Uncertain significance (Aug 14, 2024)

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