PSG1

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

Basic information

Region (hg38): 19:42866464-42879822

Previous symbols: [ "PSBG1" ]

Links

ENSG00000231924 ∙ ∙ OMIM:176390 ∙ HGNC:9514 ∙ Uniprot:P11464 ∙ 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 PSG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSG1 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						0
missense			75	8		83
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	75	8	0

Variants in PSG1

This is a list of pathogenic ClinVar variants found in the PSG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-42868110-C-T		not specified	Likely benign (Aug 02, 2021)
19-42868115-G-C		not specified	Uncertain significance (Jul 27, 2024)
19-42868117-C-G		not specified	Uncertain significance (Oct 16, 2023)
19-42868136-T-C		not specified	Uncertain significance (Apr 18, 2023)
19-42868157-A-G		not specified	Likely benign (Jul 14, 2022)
19-42868199-C-G		not specified	Likely benign (Nov 08, 2022)
19-42868257-G-C		not specified	Likely benign (Dec 15, 2022)
19-42868273-G-T		not specified	Uncertain significance (Dec 15, 2022)
19-42868277-G-A		not specified	Uncertain significance (Feb 16, 2023)
19-42868288-C-G		not specified	Uncertain significance (Mar 25, 2024)
19-42868331-T-C		not specified	Uncertain significance (Oct 27, 2022)
19-42868355-T-C		not specified	Uncertain significance (Dec 12, 2023)
19-42868762-C-T		not specified	Uncertain significance (Jun 26, 2024)
19-42868780-C-A		not specified	Uncertain significance (May 25, 2022)
19-42868785-C-T		not specified	Uncertain significance (Mar 27, 2023)
19-42868819-G-C		not specified	Likely benign (Jan 31, 2023)
19-42868842-G-A		not specified	Uncertain significance (May 16, 2024)
19-42868900-C-T		not specified	Uncertain significance (Aug 27, 2024)
19-42868916-A-C		not specified	Uncertain significance (Dec 13, 2023)
19-42868932-T-G		not specified	Uncertain significance (Jun 27, 2022)
19-42868947-C-G		not specified	Uncertain significance (Oct 08, 2024)
19-42868968-T-G		not specified	Uncertain significance (Aug 13, 2021)
19-42868978-C-G		not specified	Uncertain significance (Jan 12, 2024)
19-42868978-C-T		not specified	Uncertain significance (Dec 18, 2023)
19-42869004-T-A		not specified	Uncertain significance (Mar 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSG1	protein_coding	protein_coding	ENST00000244296	5	13359

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.62e-29	5.32e-8	124057	98	1505	125660	0.00640

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-6.11	495	233	2.13	0.0000135	2716
Missense in Polyphen		101	49.353	2.0465		673
Synonymous	-5.73	158	89.2	1.77	0.00000497	854
Loss of Function	-4.46	33	14.6	2.26	8.29e-7	172

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00192	0.00192
Ashkenazi Jewish	0.00109	0.00109
East Asian	0.0763	0.0745
Finnish	0.00	0.00
European (Non-Finnish)	0.00101	0.000959
Middle Eastern	0.0763	0.0745
South Asian	0.00295	0.00265
Other	0.00474	0.00458

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• loftool: 0.951
• rvis_EVS: 1.85
• rvis_percentile_EVS: 97.15

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.449

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;leukocyte migration
• Cellular component: extracellular region
• Molecular function: protein binding