PHYHIP

protein-coding

phytanoyl-CoA 2-hydroxylase interacting protein

Gene summary

Enables protein tyrosine kinase binding activity. Involved in intracellular protein localization. Located in mitochondrion and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

DYRK1AP3

MANE transcript

NM_014759.5

Inheritance

—

ClinVar variants

U:29

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr8:22,219,703-22,232,101

External References & Databases

Ensembl (ENSG00000168490)

Transcript & Mutation Effects

hg38 • Region Span ~12.4 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 PHYHIP variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 28

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014759.5. 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			28 clinvar			28
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	29	0	0	29

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014759.5	RefSeq	NP_055574.3	4	MANE Select
ENST00000454243.7	Ensembl	ENSP00000415491.2	4	MANE Select
NM_001099335.2	RefSeq	NP_001092805.1	4	Standard
NM_001363311.2	RefSeq	NP_001350240.1	4	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000454243
Coding exons: 4
Length: 12633
Individuals with no LoFs: 124671
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 124673
p: 0.00000802

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.26	77	210	0.367	0.0000133	2179
Missense (PolyPhen)		13	87.897	0.1479		927
Synonymous	-0.937	103	91.6	1.12	0.00000654	615
Loss of Function	2.77	1	10.8	0.0924	4.60e-7	127

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000049	0.000046	rare
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: Its interaction with PHYH suggests a role in the development of the central system.;

Recessive Scores

pRec: 0.142

Intolerance Scores

RVIS EVS: -0.6
RVIS percentile EVS: 17.75

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.654

Gene Damage Prediction

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