PHYHD1

phytanoyl-CoA dioxygenase domain containing 1

Basic information

Region (hg38): 9:128920966-128942041

Links

ENSG00000175287 ∙ NCBI:254295 ∙ OMIM:620042 ∙ HGNC:23396 ∙ Uniprot:Q5SRE7 ∙ 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 PHYHD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHYHD1 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			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in PHYHD1

This is a list of pathogenic ClinVar variants found in the PHYHD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-128927081-C-T		not specified	Uncertain significance (Sep 22, 2023)
9-128927090-G-T		not specified	Uncertain significance (Jul 09, 2021)
9-128927107-A-T		not specified	Uncertain significance (Dec 02, 2024)
9-128927111-T-C		not specified	Uncertain significance (Oct 26, 2021)
9-128927133-G-A		not specified	Uncertain significance (Mar 25, 2024)
9-128927152-C-T		not specified	Uncertain significance (Aug 21, 2023)
9-128927189-G-A		not specified	Uncertain significance (Sep 27, 2024)
9-128927195-A-G		not specified	Uncertain significance (Nov 09, 2024)
9-128933807-G-A		not specified	Uncertain significance (Jun 16, 2024)
9-128933842-G-A		not specified	Uncertain significance (Oct 25, 2024)
9-128934017-T-G		not specified	Uncertain significance (Nov 06, 2024)
9-128934033-G-T		not specified	Uncertain significance (Jun 17, 2024)
9-128936456-G-A		not specified	Uncertain significance (Nov 11, 2024)
9-128936468-G-A		not specified	Uncertain significance (Sep 23, 2023)
9-128936616-G-A		not specified	Uncertain significance (Dec 19, 2022)
9-128936629-G-A		not specified	Uncertain significance (Jan 03, 2024)
9-128940373-C-A		not specified	Uncertain significance (Feb 15, 2023)
9-128940412-G-C		not specified	Uncertain significance (Sep 27, 2022)
9-128940427-C-T		not specified	Uncertain significance (May 14, 2024)
9-128940428-G-A		not specified	Likely benign (Oct 14, 2023)
9-128940449-G-A		not specified	Uncertain significance (Sep 22, 2022)
9-128940468-G-A		not specified	Uncertain significance (Oct 17, 2023)
9-128940606-G-A		not specified	Uncertain significance (Aug 11, 2024)
9-128940623-G-A		not specified	Uncertain significance (Jul 22, 2022)
9-128940623-G-C		not specified	Uncertain significance (Apr 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHYHD1	protein_coding	protein_coding	ENST00000308941	10	21147

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.04e-13	0.0250	125542	0	206	125748	0.000819

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.231	171	180	0.952	0.0000108	1911
Missense in Polyphen		36	32.264	1.1158		408
Synonymous	-0.508	75	69.6	1.08	0.00000455	591
Loss of Function	-0.0239	19	18.9	1.01	9.43e-7	196

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00100	0.00100
Ashkenazi Jewish	0.00	0.00
East Asian	0.000544	0.000544
Finnish	0.00104	0.00102
European (Non-Finnish)	0.00110	0.00109
Middle Eastern	0.000544	0.000544
South Asian	0.000527	0.000523
Other	0.000817	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 1 has alpha-ketoglutarate-dependent dioxygenase activity. Does not show detectable activity towards fatty acid CoA thioesters. Is not expected to be active with phytanoyl CoA. Isoform 2 and isoform 3 probably lack enzyme activity. {ECO:0000269|PubMed:21530488}.

Recessive Scores

• pRec: 0.0585

Intolerance Scores

• loftool: 0.0991
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.22

Haploinsufficiency Scores

• pHI: 0.0406
• hipred: N
• hipred_score: 0.146
• ghis: 0.488

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0319

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phyhd1

Gene ontology

• Biological process: oxidation-reduction process
• Molecular function: protein binding;metal ion binding;dioxygenase activity