PHLDA1

pleckstrin homology like domain family A member 1

Basic information

Region (hg38): 12:76025447-76031776

Links

ENSG00000139289 ∙ NCBI:22822 ∙ OMIM:605335 ∙ HGNC:8933 ∙ Uniprot:Q8WV24 ∙ 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 PHLDA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHLDA1 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			32			32
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	33	0	1

Variants in PHLDA1

This is a list of pathogenic ClinVar variants found in the PHLDA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-76030588-T-G		not specified	Uncertain significance (Jul 20, 2021)
12-76030621-G-A		not specified	Uncertain significance (Jun 16, 2024)
12-76030621-G-T		not specified	Uncertain significance (Apr 20, 2024)
12-76030640-G-A		not specified	Uncertain significance (Dec 17, 2023)
12-76030651-G-A		not specified	Uncertain significance (Sep 16, 2021)
12-76030665-G-C		not specified	Uncertain significance (Sep 25, 2023)
12-76030676-G-C		not specified	Uncertain significance (May 08, 2024)
12-76030762-G-A		not specified	Uncertain significance (Sep 13, 2023)
12-76030772-G-C		not specified	Uncertain significance (Mar 27, 2023)
12-76030781-G-A		not specified	Uncertain significance (Sep 25, 2024)
12-76030817-A-T		not specified	Uncertain significance (Sep 26, 2024)
12-76030907-G-T		not specified	Uncertain significance (Dec 15, 2023)
12-76030912-G-A		not specified	Uncertain significance (Nov 27, 2024)
12-76030935-G-C		not specified	Uncertain significance (Sep 14, 2021)
12-76030982-C-T		not specified	Uncertain significance (Mar 04, 2024)
12-76030994-T-C		not specified	Uncertain significance (Oct 06, 2024)
12-76031076-G-T		not specified	Uncertain significance (Oct 26, 2022)
12-76031100-T-G		not specified	Uncertain significance (Feb 17, 2023)
12-76031157-TTGC-T			Benign (Oct 02, 2024)
12-76031257-C-A		not specified	Uncertain significance (Apr 05, 2023)
12-76031279-C-G		not specified	Uncertain significance (Nov 08, 2022)
12-76031305-C-A		not specified	Uncertain significance (Jan 27, 2025)
12-76031357-C-G		not specified	Uncertain significance (Jun 09, 2022)
12-76031421-G-T		not specified	Uncertain significance (Jul 26, 2022)
12-76031437-G-T		not specified	Uncertain significance (Feb 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHLDA1	protein_coding	protein_coding	ENST00000266671	1	8486

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.798	0.201	125581	0	2	125583	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.618	183	208	0.879	0.00000948	2524
Missense in Polyphen		49	66.704	0.73458		836
Synonymous	-1.40	111	93.8	1.18	0.00000438	828
Loss of Function	2.98	2	14.1	0.142	6.11e-7	139

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000161	0.0000905
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	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Seems to be involved in regulation of apoptosis. May be involved in detachment-mediated programmed cell death. May mediate apoptosis during neuronal development. May be involved in regulation of anti-apoptotic effects of IGF1. May be involved in translational regulation. {ECO:0000269|PubMed:11369516, ECO:0000269|PubMed:12738777}.
• Pathway: G2/M Transition;Mitotic G2-G2/M phases;Cell Cycle;Interaction between PHLDA1 and AURKA;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.134

Haploinsufficiency Scores

• pHI: 0.333
• hipred: N
• hipred_score: 0.235
• ghis: 0.414

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.958

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phlda1

Gene ontology

• Biological process: G2/M transition of mitotic cell cycle;apoptotic process;FasL biosynthetic process
• Cellular component: nucleus;nucleolus;cytosol;cytoplasmic vesicle
• Molecular function: protein binding