PDCL2

protein-coding

phosducin like 2

Gene summary

This gene encodes a member of the phosducin-like protein family and is a putative modulator of heterotrimeric G proteins. The protein shares extensive amino acid sequence homology with phosducin. Members of the phosducin-like protein family have been shown to bind to the beta-gamma subunits of G proteins. [provided by RefSeq, Jul 2008]

MANE transcript

NM_152401.3

Inheritance

—

ClinVar variants

P:1U:22

Top phenotype

Male infertility

gnomAD constraint

pLI —, LoF o/e 0.55

Max pathogenic AF

—

Genomic locus

chr4:55,556,519-55,592,245

External References & Databases

Ensembl (ENSG00000163440)

Transcript & Mutation Effects

hg38 • Region Span ~35.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PDCL2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 22

Male infertilityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152401.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			22 clinvar			22
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)	1 clinvar					1
Total	1	0	22	0	0	23

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152401.3	RefSeq	NP_689614.2	6	MANE Select
ENST00000295645.9	Ensembl	ENSP00000295645.4	6	MANE Select
ENST00000929200.1	Ensembl	ENSP00000599259.1	6	Standard
ENST00000929200.2	Ensembl	ENSP00000599259.1	6	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000295645
Coding exons: 6
Length: 35688
Individuals with no LoFs: 124573
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 124588
p: 0.0000602

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.582	88	105	0.840	0.00000497	1605
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.000073	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.178

Gene Damage Prediction

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