PLAC1

placenta enriched 1, the group of OOSP family

Basic information

Region (hg38): X:134565838-134764322

Links

ENSG00000170965 ∙ NCBI:10761 ∙ OMIM:300296 ∙ HGNC:9044 ∙ Uniprot:Q9HBJ0 ∙ 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 PLAC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLAC1 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			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	2	1

Variants in PLAC1

This is a list of pathogenic ClinVar variants found in the PLAC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-134566069-G-C		not specified	Uncertain significance (Sep 20, 2024)
X-134566084-T-C		not specified	Uncertain significance (Dec 14, 2023)
X-134566105-T-C		not specified	Uncertain significance (Aug 21, 2024)
X-134566162-G-A		not specified	Uncertain significance (Mar 30, 2024)
X-134566180-A-G		not specified	Uncertain significance (Feb 19, 2025)
X-134566244-A-G		not specified	Uncertain significance (May 29, 2024)
X-134566286-C-G		not specified	Uncertain significance (Apr 23, 2024)
X-134566323-C-G		not specified	Uncertain significance (Oct 28, 2024)
X-134566328-G-T		not specified	Uncertain significance (Feb 28, 2023)
X-134566368-C-T			Benign (May 21, 2018)
X-134566369-G-A		not specified	Uncertain significance (Jan 31, 2022)
X-134566456-C-T		not specified	Uncertain significance (Mar 18, 2024)
X-134566475-C-T		not specified	Uncertain significance (Jan 26, 2025)
X-134566476-G-A			Likely benign (Mar 01, 2022)
X-134566537-C-G		not specified	Uncertain significance (Aug 26, 2024)
X-134566541-C-G		not specified	Uncertain significance (Aug 30, 2021)
X-134566565-G-T		not specified	Uncertain significance (Aug 12, 2024)
X-134566625-C-T		not specified	Uncertain significance (Jul 27, 2021)
X-134566636-G-A		not specified	Likely benign (Jan 31, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLAC1	protein_coding	protein_coding	ENST00000359237	1	198485

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.261	74	80.6	0.918	0.00000583	1417
Missense in Polyphen		13	20.269	0.64138		347
Synonymous	-0.340	34	31.6	1.08	0.00000253	407
Loss of Function

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in placental development. {ECO:0000269|PubMed:10995572}.

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.179
• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• pHI: 0.117
• hipred: N
• hipred_score: 0.112
• ghis: 0.457

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0124

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plac1
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; cellular phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: placenta development
• Cellular component: cellular_component;extracellular region
• Molecular function: molecular_function