PHYHIP

phytanoyl-CoA 2-hydroxylase interacting protein

Basic information

Region (hg38): 8:22219702-22232101

Previous symbols: [ "DYRK1AP3" ]

Links

ENSG00000168490 ∙ NCBI:9796 ∙ OMIM:608511 ∙ HGNC:16865 ∙ Uniprot:Q92561 ∙ 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 PHYHIP gene.

• Inborn genetic diseases (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHYHIP 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in PHYHIP

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

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

Position	Type	Phenotype	Significance	ClinVar
8-22221517-G-A		not specified	Uncertain significance (Oct 06, 2021)
8-22221627-G-A		not specified	Uncertain significance (Mar 16, 2022)
8-22221700-G-C		not specified	Uncertain significance (May 08, 2023)
8-22221864-T-C		not specified	Uncertain significance (Sep 06, 2022)
8-22221877-C-T		not specified	Uncertain significance (Jun 09, 2022)
8-22224252-A-T		not specified	Uncertain significance (Sep 26, 2022)
8-22226925-T-G		not specified	Uncertain significance (Aug 23, 2021)
8-22228223-C-G		not specified	Uncertain significance (Aug 30, 2022)
8-22228319-G-T		not specified	Uncertain significance (Nov 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHYHIP	protein_coding	protein_coding	ENST00000454243	4	12633

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.860	0.140	124671	0	2	124673	0.00000802

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.26	77	210	0.367	0.0000133	2179
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000647	0.0000647
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000486	0.0000464
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: 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

Haploinsufficiency Scores

• pHI: 0.337
• hipred: Y
• hipred_score: 0.707
• ghis: 0.640

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.654

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phyhip