PSG9

pregnancy specific beta-1-glycoprotein 9, the group of V-set domain containing|Pregnancy specific glycoproteins

Basic information

Region (hg38): 19:43211790-43269530

Previous symbols: [ "PSG11" ]

Links

ENSG00000183668 ∙ NCBI:5678 ∙ OMIM:176398 ∙ HGNC:9526 ∙ Uniprot:Q00887 ∙ 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 PSG9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSG9 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			57	6	1	64
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	57	8	1

Variants in PSG9

This is a list of pathogenic ClinVar variants found in the PSG9 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-43258189-G-C			Likely benign (Jan 01, 2023)
19-43258207-A-G		not specified	Uncertain significance (Dec 13, 2023)
19-43258211-T-C		not specified	Uncertain significance (Sep 12, 2023)
19-43258218-C-G		not specified	Uncertain significance (Feb 12, 2024)
19-43258231-A-G		not specified	Uncertain significance (Sep 17, 2021)
19-43258267-G-T		not specified	Uncertain significance (Jan 23, 2024)
19-43258277-C-T			Benign (Aug 10, 2017)
19-43258307-A-G		not specified	Uncertain significance (Dec 27, 2023)
19-43258329-A-C		not specified	Uncertain significance (Apr 22, 2022)
19-43258345-G-A		not specified	Uncertain significance (Feb 12, 2024)
19-43258351-A-G		not specified	Likely benign (Jul 25, 2023)
19-43258357-T-C		not specified	Uncertain significance (Jan 04, 2024)
19-43258394-C-A		not specified	Uncertain significance (Apr 25, 2022)
19-43258438-C-A		not specified	Uncertain significance (Nov 18, 2022)
19-43258450-G-A		not specified	Uncertain significance (Nov 30, 2022)
19-43258454-C-G		not specified	Uncertain significance (Jun 03, 2022)
19-43258865-T-A		not specified	Uncertain significance (Apr 09, 2024)
19-43258878-G-A		not specified	Uncertain significance (Apr 07, 2022)
19-43258886-C-A		not specified	Uncertain significance (Feb 16, 2023)
19-43258899-A-C		not specified	Uncertain significance (Dec 17, 2023)
19-43258901-C-T		not specified	Uncertain significance (Jun 17, 2022)
19-43258910-A-G		not specified	Uncertain significance (Jun 22, 2023)
19-43258949-C-T		not specified	Uncertain significance (Aug 16, 2021)
19-43258982-C-G		not specified	Uncertain significance (Jun 05, 2024)
19-43259009-C-T		not specified	Uncertain significance (Apr 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSG9	protein_coding	protein_coding	ENST00000270077	6	57740

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.87e-22	0.0000447	101009	2422	22316	125747	0.104

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.92	359	234	1.54	0.0000131	2731
Missense in Polyphen		77	65.773	1.1707		905
Synonymous	-5.43	156	90.3	1.73	0.00000517	841
Loss of Function	-1.67	28	20.0	1.40	0.00000119	226

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.346	0.344
Ashkenazi Jewish	0.0812	0.0671
East Asian	0.369	0.355
Finnish	0.0897	0.0834
European (Non-Finnish)	0.0639	0.0598
Middle Eastern	0.369	0.355
South Asian	0.0989	0.0852
Other	0.100	0.0927

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• loftool: 0.962
• rvis_EVS: 1.61
• rvis_percentile_EVS: 95.92

Haploinsufficiency Scores

• pHI: 0.250
• hipred: N
• hipred_score: 0.112
• ghis: 0.414

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.566

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