BPHL

biphenyl hydrolase like

Basic information

Region (hg38): 6:3118373-3153578

Previous symbols: [ "MCNAA" ]

Links

ENSG00000137274 ∙ NCBI:670 ∙ OMIM:603156 ∙ HGNC:1094 ∙ Uniprot:Q86WA6 ∙ 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 BPHL gene.

• Inborn genetic diseases (11 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BPHL 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			10	1	1	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	10	2	2

Variants in BPHL

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

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

Position	Type	Phenotype	Significance	ClinVar
6-3118775-G-T		not specified	Uncertain significance (Jan 09, 2024)
6-3118815-C-A		not specified	Uncertain significance (Sep 26, 2023)
6-3127284-A-G		not specified	Uncertain significance (Sep 25, 2023)
6-3127371-T-C		not specified	Uncertain significance (Mar 31, 2022)
6-3129046-C-T			Benign (May 19, 2018)
6-3129053-G-A			Likely benign (Jul 01, 2022)
6-3129067-C-G		not specified	Uncertain significance (Feb 16, 2023)
6-3129102-C-T		not specified	Uncertain significance (Oct 03, 2023)
6-3129156-G-A		not specified	Uncertain significance (Aug 02, 2022)
6-3129172-C-G		not specified	Uncertain significance (Jan 19, 2024)
6-3129177-G-A		not specified	Uncertain significance (May 25, 2022)
6-3129183-A-G		not specified	Uncertain significance (Nov 01, 2022)
6-3129196-A-G		not specified	Uncertain significance (Aug 16, 2022)
6-3137488-C-G		not specified	Uncertain significance (Apr 08, 2022)
6-3140413-G-A		not specified	Likely benign (Apr 07, 2023)
6-3140427-G-T		not specified	Uncertain significance (Jan 09, 2024)
6-3140434-T-C		not specified	Uncertain significance (Sep 30, 2021)
6-3140466-C-T		not specified	Uncertain significance (Feb 28, 2024)
6-3152528-C-T		not specified	Uncertain significance (Apr 07, 2023)
6-3152559-A-T		not specified	Uncertain significance (Aug 08, 2022)
6-3153540-A-C			Benign (Jul 15, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BPHL	protein_coding	protein_coding	ENST00000380379	7	35205

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.58e-7	0.399	123246	157	2345	125748	0.0100

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.421	140	155	0.905	0.00000885	1879
Missense in Polyphen		49	46.3	1.0583		523
Synonymous	0.776	54	61.8	0.874	0.00000401	582
Loss of Function	0.626	11	13.5	0.816	7.21e-7	161

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.146	0.144
Ashkenazi Jewish	0.00	0.00
East Asian	0.00163	0.00158
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000464	0.000457
Middle Eastern	0.00163	0.00158
South Asian	0.00297	0.00288
Other	0.00521	0.00490

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine hydrolase that catalyzes the hydrolytic activation of amino acid ester prodrugs of nucleoside analogs such as valacyclovir and valganciclovir. Activates valacyclovir to acyclovir. May play a role in detoxification processes. It is a specific alpha-amino acid ester hydrolase that prefers small, hydrophobic, and aromatic side chains and does not have a stringent requirement for the leaving group other than preferring a primary alcohol. {ECO:0000269|PubMed:18256025}.
• Pathway: Phase I - Functionalization of compounds;Biological oxidations;Metabolism (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.719
• rvis_EVS: 0.73
• rvis_percentile_EVS: 86.17

Haploinsufficiency Scores

• pHI: 0.140
• hipred: N
• hipred_score: 0.204
• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.278

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bphl
• Phenotype: homeostasis/metabolism phenotype; limbs/digits/tail phenotype; hearing/vestibular/ear phenotype

Gene ontology

• Biological process: cellular amino acid metabolic process;xenobiotic metabolic process;response to toxic substance
• Cellular component: mitochondrion;mitochondrial outer membrane
• Molecular function: alpha-amino-acid esterase activity