PDCL2

phosducin like 2

Basic information

Region (hg38): 4:55556519-55592245

Links

ENSG00000163440 ∙ NCBI:132954 ∙ OMIM:611676 ∙ HGNC:29524 ∙ Uniprot:Q8N4E4 ∙ 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 PDCL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDCL2 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in PDCL2

This is a list of pathogenic ClinVar variants found in the PDCL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-55556609-G-A		not specified	Uncertain significance (Nov 11, 2024)
4-55556625-A-G		not specified	Uncertain significance (May 02, 2024)
4-55562419-T-G		not specified	Uncertain significance (Dec 04, 2024)
4-55562479-C-T		not specified	Uncertain significance (Nov 14, 2023)
4-55562484-A-G		not specified	Uncertain significance (Jul 27, 2024)
4-55562487-G-A		not specified	Uncertain significance (Apr 09, 2024)
4-55562511-T-A		not specified	Uncertain significance (Mar 08, 2024)
4-55562530-C-T		not specified	Uncertain significance (Dec 09, 2023)
4-55562605-T-C		not specified	Uncertain significance (Nov 09, 2021)
4-55569802-C-G		not specified	Uncertain significance (Dec 24, 2024)
4-55580843-T-C		not specified	Uncertain significance (Apr 30, 2024)
4-55580894-T-C		not specified	Uncertain significance (Jun 28, 2024)
4-55580912-C-T		Male infertility	Pathogenic (Dec 18, 2023)
4-55582129-T-C		not specified	Uncertain significance (Oct 28, 2023)
4-55582137-C-G		not specified	Uncertain significance (Jul 10, 2024)
4-55582192-C-T		not specified	Uncertain significance (Feb 14, 2023)
4-55582201-T-C		not specified	Uncertain significance (Jun 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDCL2	protein_coding	protein_coding	ENST00000295645	6	35688

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00146	0.885	124573	0	15	124588	0.0000602

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.582	88	105	0.840	0.00000497	1605
Missense in Polyphen		44	45.983	0.95687		682
Synonymous	1.70	20	32.3	0.620	0.00000152	384
Loss of Function	1.37	6	10.9	0.551	4.60e-7	171

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000293	0.0000293
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000116	0.000106
Middle Eastern	0.00	0.00
South Asian	0.0000735	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in germ cell maturation. {ECO:0000250}.

Recessive Scores

• pRec: 0.0992

Intolerance Scores

• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.95

Haploinsufficiency Scores

• pHI: 0.240
• hipred: N
• hipred_score: 0.231
• ghis: 0.400

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.178

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdcl2