POGK

pogo transposable element derived with KRAB domain, the group of DNA transposon derived genes|Helix-turn-helix CENPB type domain containing

Basic information

Region (hg38): 1:166839447-166856359

Links

ENSG00000143157 ∙ NCBI:57645 ∙ OMIM:620039 ∙ HGNC:18800 ∙ Uniprot:Q9P215 ∙ 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 POGK gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POGK 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
missense			31			31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	0	1

Variants in POGK

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

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

Position	Type	Phenotype	Significance	ClinVar
1-166840967-C-T		not specified	Uncertain significance (Jul 22, 2024)
1-166840969-G-T		not specified	Uncertain significance (Dec 01, 2022)
1-166840979-T-G		not specified	Uncertain significance (Mar 01, 2023)
1-166840989-C-A		not specified	Uncertain significance (Dec 21, 2023)
1-166841007-G-C		not specified	Uncertain significance (Feb 19, 2025)
1-166846648-T-A		not specified	Uncertain significance (May 31, 2023)
1-166846696-C-T		not specified	Uncertain significance (Aug 02, 2023)
1-166846709-G-A		not specified	Uncertain significance (Dec 19, 2022)
1-166847527-G-A		not specified	Uncertain significance (Feb 07, 2025)
1-166848967-G-T		not specified	Uncertain significance (Jun 05, 2023)
1-166848982-A-G		not specified	Uncertain significance (Aug 12, 2024)
1-166849037-G-A		not specified	Uncertain significance (Oct 30, 2023)
1-166849046-G-A		not specified	Uncertain significance (May 05, 2023)
1-166849085-C-G		not specified	Uncertain significance (Feb 25, 2025)
1-166849099-A-G		not specified	Uncertain significance (Jan 16, 2025)
1-166849112-G-C		not specified	Uncertain significance (Oct 29, 2021)
1-166849142-G-A		not specified	Uncertain significance (Jul 05, 2024)
1-166849158-C-A		not specified	Uncertain significance (Jul 12, 2023)
1-166849313-A-G		not specified	Uncertain significance (May 23, 2024)
1-166849322-G-A		not specified	Uncertain significance (Feb 16, 2023)
1-166849334-G-A		not specified	Uncertain significance (Jul 27, 2024)
1-166849343-A-G		not specified	Uncertain significance (Apr 07, 2023)
1-166849449-C-T			Benign (Apr 24, 2018)
1-166849531-G-A		not specified	Uncertain significance (Jun 12, 2023)
1-166849597-G-T		not specified	Uncertain significance (Aug 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POGK	protein_coding	protein_coding	ENST00000367875	4	16901

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.892	0.108	125741	0	4	125745	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.35	193	376	0.514	0.0000228	4026
Missense in Polyphen		88	204.66	0.42999		2151
Synonymous	1.57	127	152	0.838	0.00000963	1180
Loss of Function	3.87	4	24.8	0.161	0.00000143	252

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000881	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.170
• rvis_EVS: 0.71
• rvis_percentile_EVS: 85.63

Haploinsufficiency Scores

• pHI: 0.184
• hipred: Y
• hipred_score: 0.675
• ghis: 0.422

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.885

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pogk

Gene ontology

• Biological process: regulation of transcription, DNA-templated;multicellular organism development
• Cellular component: nucleus
• Molecular function: DNA binding;protein binding