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.

• not_specified (48 variants)

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. These statistics are base on transcript: NM_000007350.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			48			48
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	48	0	0

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