PSG5

pregnancy specific beta-1-glycoprotein 5, the group of Pregnancy specific glycoproteins|V-set domain containing

Basic information

Region (hg38): 19:43166256-43186536

Links

ENSG00000204941 ∙ NCBI:5673 ∙ OMIM:176394 ∙ HGNC:9522 ∙ Uniprot:Q15238 ∙ 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 PSG5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSG5 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				2		2
missense			49	5		54
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	49	7	0

Variants in PSG5

This is a list of pathogenic ClinVar variants found in the PSG5 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-43170111-A-C		not specified	Uncertain significance (Nov 13, 2024)
19-43170120-C-T		not specified	Likely benign (Jun 09, 2022)
19-43170133-A-G		not specified	Uncertain significance (Oct 19, 2024)
19-43170135-G-A		not specified	Uncertain significance (Feb 01, 2025)
19-43175258-A-G			Likely benign (Jul 21, 2018)
19-43175262-G-A		not specified	Uncertain significance (Oct 14, 2023)
19-43175269-G-A		not specified	Uncertain significance (Jul 14, 2021)
19-43175278-A-G		not specified	Uncertain significance (Feb 16, 2023)
19-43175297-C-A		not specified	Uncertain significance (Dec 07, 2024)
19-43175319-G-A		not specified	Uncertain significance (Dec 10, 2024)
19-43175350-C-T		not specified	Uncertain significance (Apr 27, 2024)
19-43175353-T-A		not specified	Uncertain significance (Jan 09, 2024)
19-43175374-C-G		not specified	Uncertain significance (Sep 11, 2024)
19-43175382-T-C		not specified	Uncertain significance (May 05, 2022)
19-43175385-G-C		not specified	Uncertain significance (Apr 19, 2023)
19-43175404-A-C		not specified	Uncertain significance (Jan 24, 2025)
19-43175406-T-C		not specified	Uncertain significance (Jul 16, 2024)
19-43175450-G-T		not specified	Likely benign (Feb 24, 2025)
19-43175873-G-A		not specified	Uncertain significance (Jul 25, 2024)
19-43175920-C-T		not specified	Uncertain significance (Oct 06, 2021)
19-43175935-T-C		not specified	Uncertain significance (Jul 14, 2024)
19-43175962-C-T		not specified	Uncertain significance (Dec 07, 2024)
19-43175986-T-G		not specified	Uncertain significance (Jan 25, 2025)
19-43175992-G-A		not specified	Uncertain significance (Mar 23, 2022)
19-43176016-G-A		not specified	Uncertain significance (May 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSG5	protein_coding	protein_coding	ENST00000366175	5	20281

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.82e-22	0.0000377	125589	0	34	125623	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-3.76	313	173	1.80	0.00000971	2110
Missense in Polyphen		103	67.853	1.518		880
Synonymous	-5.27	123	67.8	1.81	0.00000374	684
Loss of Function	-1.91	27	18.2	1.48	0.00000126	196

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000205	0.000205
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000193	0.000185
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000982	0.0000980
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• loftool: 0.951
• rvis_EVS: 2.73
• rvis_percentile_EVS: 98.96

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: 0.225

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: protein binding