PHLDA1

protein-coding

pleckstrin homology like domain family A member 1

Gene summary

This gene encodes an evolutionarily conserved proline-histidine rich nuclear protein. The encoded protein may play an important role in the anti-apoptotic effects of insulin-like growth factor-1. [provided by RefSeq, Jul 2008]

MANE transcript

NM_007350.3

Inheritance

—

ClinVar variants

U:58

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.14

Max pathogenic AF

—

Genomic locus

chr12:76,025,447-76,031,776

External References & Databases

Ensembl (ENSG00000139289)

Transcript & Mutation Effects

hg38 • Region Span ~6.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PHLDA1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 57

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007350.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			58 clinvar			58
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	58	0	0	58

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007350.3	RefSeq	NP_031376.3	1	MANE Select
ENST00000266671.10	Ensembl	ENSP00000266671.5	1	MANE Select
ENST00000602540.5	Ensembl	ENSP00000473593.1	1	Standard
ENST00001138329.1	Ensembl	ENSP00000803860.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

G2/M Transition
Mitotic G2-G2/M phases
Cell Cycle
Interaction between PHLDA1 and AURKA
Cell Cycle, Mitotic

Biological Process

G2/M transition of mitotic cell cycle
apoptotic process
FasL biosynthetic process

Molecular Function

protein binding

Cellular Component

nucleus
nucleolus
cytosol
cytoplasmic vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000266671
Coding exons: 1
Length: 8486
Individuals with no LoFs: 125581
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125583
p: 0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.618	183	208	0.879	0.00000948	2524
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.134

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.958

Gene Damage Prediction

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