PHLDA2

pleckstrin homology like domain family A member 2, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 11:2928272-2929420

Previous symbols: [ "TSSC3" ]

Links

ENSG00000181649 ∙ NCBI:7262 ∙ OMIM:602131 ∙ HGNC:12385 ∙ Uniprot:Q53GA4 ∙ 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 PHLDA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHLDA2 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			10	2		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	2	0

Variants in PHLDA2

This is a list of pathogenic ClinVar variants found in the PHLDA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-2928953-A-T		not specified	Uncertain significance (Sep 16, 2021)
11-2929013-C-T		not specified	Uncertain significance (Nov 07, 2022)
11-2929028-G-T		not specified	Uncertain significance (Mar 15, 2024)
11-2929039-T-C		not specified	Uncertain significance (Feb 13, 2024)
11-2929052-G-A		not specified	Uncertain significance (Jun 05, 2023)
11-2929056-G-T		not specified	Uncertain significance (Aug 08, 2023)
11-2929059-C-G		not specified	Uncertain significance (Jan 17, 2024)
11-2929082-C-T		not specified	Likely benign (Jul 14, 2021)
11-2929135-T-C		not specified	Likely benign (Apr 07, 2023)
11-2929228-C-T		not specified	Uncertain significance (Apr 25, 2022)
11-2929246-G-C		not specified	Uncertain significance (Jul 05, 2023)
11-2929324-T-G		not specified	Uncertain significance (Dec 04, 2023)
11-2929343-G-C		not specified	Uncertain significance (Aug 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHLDA2	protein_coding	protein_coding	ENST00000314222	1	1183

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.150	0.647	119428	0	2	119430	0.00000837

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.125	86	89.3	0.963	0.00000402	973
Missense in Polyphen		27	31.998	0.8438		345
Synonymous	0.152	38	39.2	0.969	0.00000186	318
Loss of Function	0.685	1	2.06	0.485	8.78e-8	26

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000671	0.0000671
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in regulating placenta growth. May act via its PH domain that competes with other PH domain-containing proteins, thereby preventing their binding to membrane lipids (By similarity). {ECO:0000250}.

Intolerance Scores

• loftool: 0.307
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

• pHI: 0.100
• hipred: N
• hipred_score: 0.314
• ghis: 0.594

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.932

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phlda2
• Phenotype: embryo phenotype; cellular phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: apoptotic process
• Cellular component: cytoplasm;membrane