PHYHIPL

phytanoyl-CoA 2-hydroxylase interacting protein like, the group of Fibronectin type III domain containing

Basic information

Region (hg38): 10:59176642-59247774

Links

ENSG00000165443 ∙ NCBI:84457 ∙ ∙ HGNC:29378 ∙ Uniprot:Q96FC7 ∙ 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 PHYHIPL gene.

• Inborn genetic diseases (12 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHYHIPL 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				1		1
missense			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	0

Variants in PHYHIPL

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

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

Position	Type	Phenotype	Significance	ClinVar
10-59176872-G-A		not specified	Uncertain significance (Jan 26, 2023)
10-59176905-G-A		not specified	Uncertain significance (Sep 15, 2021)
10-59176909-A-C		not specified	Uncertain significance (Feb 10, 2022)
10-59176951-A-T		not specified	Uncertain significance (Aug 12, 2021)
10-59234490-T-G		not specified	Uncertain significance (Jul 12, 2022)
10-59245208-T-C		not specified	Uncertain significance (Jan 16, 2024)
10-59245244-C-T		not specified	Uncertain significance (Nov 17, 2022)
10-59245260-A-T		not specified	Uncertain significance (Nov 30, 2022)
10-59245342-A-C		not specified	Uncertain significance (Jun 13, 2023)
10-59245355-C-T		not specified	Uncertain significance (Jun 18, 2021)
10-59245444-C-T			Likely benign (Feb 01, 2023)
10-59245574-A-G		not specified	Uncertain significance (May 24, 2023)
10-59245584-G-A		not specified	Uncertain significance (May 08, 2023)
10-59245586-C-T		not specified	Uncertain significance (Mar 13, 2023)
10-59247701-A-C		not specified	Uncertain significance (Nov 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHYHIPL	protein_coding	protein_coding	ENST00000373880	5	71185

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.821	0.179	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.64	139	205	0.678	0.0000101	2502
Missense in Polyphen		28	76.537	0.36584		937
Synonymous	-1.09	81	69.5	1.17	0.00000335	679
Loss of Function	3.03	2	14.4	0.138	6.69e-7	202

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000217	0.000214
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000442	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the development of the central system. {ECO:0000250}.

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.355
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.64

Haploinsufficiency Scores

• pHI: 0.232
• hipred: Y
• hipred_score: 0.680
• ghis: 0.600

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phyhipl

Gene ontology

• Cellular component: cytoplasm