PCBD2

pterin-4 alpha-carbinolamine dehydratase 2, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 5:134905120-135007959

Links

ENSG00000132570 ∙ NCBI:84105 ∙ OMIM:609836 ∙ HGNC:24474 ∙ Uniprot:Q9H0N5 ∙ 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 PCBD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCBD2 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			5	1		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			5	1		6
Total	0	0	10	2	0

Variants in PCBD2

This is a list of pathogenic ClinVar variants found in the PCBD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-134905215-G-A		not specified	Uncertain significance (Jan 23, 2024)
5-134910344-A-G		not specified	Likely benign (Sep 17, 2021)
5-134910360-C-T		not specified	Uncertain significance (Dec 05, 2022)
5-134910423-G-T		not specified	Uncertain significance (May 06, 2024)
5-134910454-C-G		not specified	Uncertain significance (May 01, 2023)
5-134959056-C-G		not specified	Uncertain significance (Oct 29, 2021)
5-134959071-A-T		not specified	Uncertain significance (Nov 21, 2024)
5-134960608-A-G		not specified	Uncertain significance (Sep 20, 2024)
5-134960664-G-C		not specified	Uncertain significance (Jan 10, 2023)
5-134968004-C-T		not specified	Uncertain significance (Jul 07, 2024)
5-134968007-C-T		not specified	Uncertain significance (Sep 14, 2022)
5-134968020-C-T		not specified	Uncertain significance (Sep 14, 2023)
5-134968021-G-C			Likely benign (Oct 01, 2024)
5-134968024-A-T		not specified	Uncertain significance (Aug 09, 2021)
5-134968032-C-G		not specified	Uncertain significance (Dec 08, 2023)
5-134968052-A-G		not specified	Likely benign (Nov 28, 2023)
5-134968056-C-T		not specified	Uncertain significance (Aug 08, 2023)
5-134968077-T-A		not specified	Uncertain significance (Apr 26, 2024)
5-134970073-G-A		not specified	Uncertain significance (Oct 01, 2024)
5-134996330-G-A		not specified	Uncertain significance (Jul 14, 2022)
5-134996357-G-A		not specified	Uncertain significance (Dec 22, 2023)
5-134996384-A-G		not specified	Uncertain significance (Jul 30, 2023)
5-134996390-G-A		not specified	Likely benign (Jun 18, 2021)
5-134996409-C-T		not specified	Uncertain significance (Jul 25, 2024)
5-134996423-A-C		not specified	Uncertain significance (Jul 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCBD2	protein_coding	protein_coding	ENST00000512783	4	103054

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0260	0.801	124787	0	4	124791	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.179	48	51.6	0.930	0.00000229	839
Missense in Polyphen		23	24.803	0.92732		341
Synonymous	-0.944	23	17.9	1.28	8.58e-7	256
Loss of Function	1.02	3	5.62	0.534	2.37e-7	81

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000646	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000177
Middle Eastern	0.0000556	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in tetrahydrobiopterin biosynthesis. Seems to both prevent the formation of 7-pterins and accelerate the formation of quinonoid-BH2 (By similarity). {ECO:0000250}.
• Pathway: Folate biosynthesis - Homo sapiens (human);phenylalanine degradation/tyrosine biosynthesis;Biopterin metabolism (Consensus)

Recessive Scores

• pRec: 0.0987

Intolerance Scores

• loftool: 0.664
• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.43

Haploinsufficiency Scores

• pHI: 0.139
• hipred: N
• hipred_score: 0.270
• ghis: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.855

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcbd2

Gene ontology

• Biological process: tetrahydrobiopterin biosynthetic process;positive regulation of transcription, DNA-templated;protein homotetramerization;protein heterooligomerization;oxidation-reduction process
• Cellular component: cellular_component;nucleus
• Molecular function: phenylalanine 4-monooxygenase activity;protein binding;4-alpha-hydroxytetrahydrobiopterin dehydratase activity