POPDC3

popeye domain containing 3

Basic information

Region (hg38): 6:105157900-105180014

Links

ENSG00000132429 ∙ NCBI:64208 ∙ OMIM:605824 ∙ HGNC:17649 ∙ Uniprot:Q9HBV1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• muscular dystrophy, limb-girdle, autosomal recessive 26 (Limited), mode of inheritance: AR
• muscular dystrophy, limb-girdle, autosomal recessive 26 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Muscular dystrophy, limb-girdle, autosomal recessive 26	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal	31610034

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the POPDC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POPDC3 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	2	3
missense			11	1	2	14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					3	3
Total	0	0	11	2	7

Variants in POPDC3

This is a list of pathogenic ClinVar variants found in the POPDC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-105158526-G-A		not specified	Uncertain significance (Feb 27, 2024)
6-105158564-C-T		Muscular dystrophy, limb-girdle, autosomal recessive 26	Pathogenic (Apr 21, 2020)
6-105158675-T-C		not specified	Uncertain significance (Aug 30, 2022)
6-105158695-T-A		Muscular dystrophy, limb-girdle, autosomal recessive 26	Pathogenic (Apr 21, 2020)
6-105158751-C-G		not specified	Uncertain significance (Oct 20, 2023)
6-105158927-G-A			Benign (May 14, 2021)
6-105159789-C-T			Benign (May 04, 2021)
6-105159797-C-T		not specified	Uncertain significance (Feb 27, 2023)
6-105159805-A-G		not specified	Uncertain significance (Oct 06, 2021)
6-105159820-C-T		Muscular dystrophy, limb-girdle, autosomal recessive 26	Pathogenic (Apr 11, 2024)
6-105159825-A-T		Muscular dystrophy, limb-girdle, autosomal recessive 26	Pathogenic (Apr 11, 2024)
6-105161261-T-C			Benign (May 14, 2021)
6-105161325-C-T			Benign (May 22, 2021)
6-105161446-A-T		Muscular dystrophy, limb-girdle, autosomal recessive 26	Pathogenic (Apr 21, 2020)
6-105161450-T-C		Muscular dystrophy, limb-girdle, autosomal recessive 26	Pathogenic (Apr 11, 2024)
6-105161515-C-T			Benign (Jul 15, 2018)
6-105161521-G-A		not specified	Uncertain significance (Apr 27, 2022)
6-105161593-C-T			Benign (May 05, 2021)
6-105161627-T-C		not specified	Uncertain significance (Apr 05, 2023)
6-105161633-C-T		not specified	Uncertain significance (Apr 05, 2023)
6-105161640-C-T			Likely benign (Jul 01, 2024)
6-105161664-A-C		not specified	Uncertain significance (Apr 27, 2022)
6-105161678-A-G		not specified	Uncertain significance (Mar 13, 2023)
6-105161835-G-A		POPDC3-related disorder	Likely benign (Nov 04, 2021)
6-105161873-C-T		not specified	Uncertain significance (May 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POPDC3	protein_coding	protein_coding	ENST00000254765	3	21716

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0109	0.951	125715	0	24	125739	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.666	133	156	0.850	0.00000791	1898
Missense in Polyphen		50	62.902	0.79488		754
Synonymous	-0.431	61	56.9	1.07	0.00000274	568
Loss of Function	1.81	5	11.7	0.429	6.43e-7	136

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000428	0.000427
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000882	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the maintenance of heart function mediated, at least in part, through cAMP-binding. {ECO:0000250|UniProtKB:Q9ES81, ECO:0000269|PubMed:10882522}.

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.636
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.21

Haploinsufficiency Scores

• pHI: 0.185
• hipred: N
• hipred_score: 0.350
• ghis: 0.505

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.324

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Popdc3
• Phenotype: immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype

Gene ontology

• Biological process: heart development;skeletal muscle tissue development;biological_process;regulation of membrane potential;striated muscle cell differentiation
• Cellular component: membrane;integral component of membrane;sarcolemma
• Molecular function: molecular_function;cAMP binding