PSG4

pregnancy specific beta-1-glycoprotein 4, the group of V-set domain containing|Pregnancy specific glycoproteins

Basic information

Region (hg38): 19:43192702-43207299

Links

ENSG00000243137 ∙ NCBI:5672 ∙ OMIM:176393 ∙ HGNC:9521 ∙ Uniprot:Q00888 ∙ 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 PSG4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSG4 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	2	3
missense			65	5	2	72
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	65	7	4

Variants in PSG4

This is a list of pathogenic ClinVar variants found in the PSG4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-43193382-A-G			Likely benign (Jan 01, 2023)
19-43194345-A-T		not specified	Uncertain significance (Sep 26, 2023)
19-43194361-A-G		not specified	Uncertain significance (Jan 21, 2025)
19-43194393-C-T		not specified	Uncertain significance (May 01, 2024)
19-43194409-A-G		not specified	Uncertain significance (Jun 18, 2021)
19-43194412-G-A		not specified	Uncertain significance (Aug 08, 2022)
19-43194417-C-G		not specified	Uncertain significance (Jan 24, 2025)
19-43194441-A-G		not specified	Uncertain significance (Jun 26, 2024)
19-43194456-C-T		not specified	Uncertain significance (Feb 09, 2025)
19-43194469-A-T		not specified	Uncertain significance (Nov 20, 2024)
19-43194493-A-G		not specified	Uncertain significance (May 23, 2024)
19-43194501-C-T		not specified	Uncertain significance (Oct 22, 2021)
19-43194502-G-C		not specified	Uncertain significance (Jan 26, 2022)
19-43194512-C-G		not specified	Likely benign (Sep 01, 2024)
19-43194514-C-T		not specified	Uncertain significance (Feb 12, 2025)
19-43194517-C-T		not specified	Uncertain significance (Feb 06, 2023)
19-43194532-A-C		not specified	Uncertain significance (Nov 25, 2024)
19-43194573-A-G		not specified	Uncertain significance (Mar 25, 2024)
19-43194575-G-T		not specified	Likely benign (Mar 15, 2024)
19-43194588-G-A		not specified	Uncertain significance (Dec 13, 2022)
19-43195007-G-C		not specified	Uncertain significance (Sep 26, 2024)
19-43195025-G-T		not specified	Uncertain significance (Jan 03, 2024)
19-43195030-C-G		not specified	Uncertain significance (Jun 16, 2024)
19-43195058-G-C		not specified	Uncertain significance (Oct 04, 2022)
19-43195067-C-T		not specified	Uncertain significance (Feb 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSG4	protein_coding	protein_coding	ENST00000405312	6	14598

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.91e-29	4.23e-7	125658	2	24	125684	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-4.21	403	225	1.79	0.0000124	2669
Missense in Polyphen		134	81.961	1.6349		1042
Synonymous	-6.23	158	84.9	1.86	0.00000442	835
Loss of Function	-2.74	35	21.3	1.64	0.00000137	226

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000122	0.000121
Ashkenazi Jewish	0.00	0.00
East Asian	0.000128	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000155	0.000141
Middle Eastern	0.000128	0.000109
South Asian	0.000205	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• loftool: 0.960
• rvis_EVS: 2.18
• rvis_percentile_EVS: 98.08

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.239

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