PSG6

pregnancy specific beta-1-glycoprotein 6, the group of V-set domain containing|Pregnancy specific glycoproteins

Basic information

Region (hg38): 19:42902085-42919563

Links

ENSG00000170848 ∙ NCBI:5675 ∙ OMIM:176395 ∙ HGNC:9523 ∙ Uniprot:Q00889 ∙ 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 PSG6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSG6 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	2
missense			45	7	2	54
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	45	8	4

Variants in PSG6

This is a list of pathogenic ClinVar variants found in the PSG6 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-42903725-CA-C			Benign (Dec 30, 2023)
19-42906937-T-C		not specified	Uncertain significance (Mar 07, 2023)
19-42906951-A-C			Likely benign (Mar 01, 2023)
19-42906957-T-A			Likely benign (Mar 01, 2023)
19-42906990-T-C		not specified	Uncertain significance (Dec 07, 2021)
19-42906997-C-T		not specified	Uncertain significance (Jul 09, 2021)
19-42907026-A-G		not specified	Likely benign (Mar 25, 2024)
19-42907038-C-T		not specified	Uncertain significance (Apr 01, 2024)
19-42907094-G-T		not specified	Uncertain significance (May 17, 2023)
19-42907117-G-A		not specified	Uncertain significance (Jun 02, 2023)
19-42907131-C-T			Likely benign (Mar 01, 2023)
19-42907578-A-C		not specified	Uncertain significance (Apr 07, 2022)
19-42907611-C-G		not specified	Uncertain significance (Jul 09, 2021)
19-42907628-T-C		not specified	Uncertain significance (Jun 18, 2024)
19-42907672-G-A		not specified	Uncertain significance (May 18, 2022)
19-42907695-A-G		not specified	Uncertain significance (Jul 09, 2021)
19-42907698-G-C		not specified	Uncertain significance (Dec 20, 2021)
19-42907698-G-T		not specified	Uncertain significance (Oct 17, 2023)
19-42907713-G-A		not specified	Uncertain significance (Oct 18, 2021)
19-42907723-G-T		not specified	Uncertain significance (Oct 03, 2022)
19-42907728-C-T		not specified	Uncertain significance (Jun 27, 2022)
19-42907765-G-A		not specified	Uncertain significance (Mar 11, 2022)
19-42907783-T-A		not specified	Uncertain significance (Aug 22, 2023)
19-42907795-C-T		not specified	Uncertain significance (Jan 17, 2024)
19-42907802-C-A		not specified	Likely benign (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSG6	protein_coding	protein_coding	ENST00000292125	6	17485

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.82e-22	0.0000509	125527	1	125	125653	0.000502

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-5.16	443	225	1.97	0.0000131	2760
Missense in Polyphen		107	65.31	1.6383		915
Synonymous	-7.33	174	87.0	2.00	0.00000480	880
Loss of Function	-1.61	28	20.2	1.39	0.00000135	226

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00228	0.00225
Ashkenazi Jewish	0.0000996	0.0000993
East Asian	0.000548	0.000545
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.0000967
Middle Eastern	0.000548	0.000545
South Asian	0.00181	0.00180
Other	0.000654	0.000653

dbNSFP

Source: dbNSFP

• Pathway: Cell surface interactions at the vascular wall;Hemostasis (Consensus)

Intolerance Scores

• loftool: 0.964
• rvis_EVS: 2.17
• rvis_percentile_EVS: 98.03

Haploinsufficiency Scores

• pHI: 0.263
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.132

Gene Damage Prediction

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

Gene ontology

• Biological process: female pregnancy
• Cellular component: extracellular region
• Molecular function: molecular_function