POPDC2

popeye domain containing 2

Basic information

Region (hg38): 3:119636457-119665324

Links

ENSG00000121577 ∙ NCBI:64091 ∙ OMIM:605823 ∙ HGNC:17648 ∙ Uniprot:Q9HBU9 ∙ 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 POPDC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POPDC2 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			40			40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	0	0

Variants in POPDC2

This is a list of pathogenic ClinVar variants found in the POPDC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-119642489-G-A		not specified	Uncertain significance (Dec 17, 2023)
3-119642507-G-C		not specified	Uncertain significance (Aug 07, 2024)
3-119648296-G-A		not specified	Uncertain significance (Jun 29, 2023)
3-119648368-G-C		not specified	Uncertain significance (Jan 09, 2024)
3-119648410-C-T		not specified	Uncertain significance (Oct 12, 2022)
3-119648417-C-G		not specified	Uncertain significance (Jul 28, 2024)
3-119648481-C-T		not specified	Uncertain significance (Jul 21, 2021)
3-119648482-G-A		not specified	Uncertain significance (Oct 19, 2024)
3-119648493-C-T		not specified	Uncertain significance (Aug 05, 2024)
3-119648568-G-A		not specified	Uncertain significance (Feb 27, 2024)
3-119648584-T-G		not specified	Uncertain significance (Feb 20, 2025)
3-119648589-C-T		not specified	Uncertain significance (Dec 03, 2024)
3-119648609-A-C		not specified	Uncertain significance (Mar 31, 2022)
3-119648610-T-C		not specified	Uncertain significance (Feb 26, 2024)
3-119648610-T-G		not specified	Uncertain significance (Feb 10, 2022)
3-119648623-G-A		not specified	Uncertain significance (Dec 22, 2024)
3-119648626-G-A		not specified	Uncertain significance (Oct 07, 2024)
3-119648658-G-C		not specified	Uncertain significance (Mar 07, 2024)
3-119654507-G-T		not specified	Uncertain significance (Nov 25, 2024)
3-119654525-A-G		not specified	Uncertain significance (Aug 02, 2023)
3-119654544-C-A		not specified	Uncertain significance (Jun 26, 2024)
3-119654608-C-A		not specified	Uncertain significance (Dec 27, 2023)
3-119654609-G-A		not specified	Uncertain significance (May 10, 2022)
3-119659958-G-A		not specified	Uncertain significance (Feb 12, 2025)
3-119659994-G-T		not specified	Uncertain significance (Apr 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POPDC2	protein_coding	protein_coding	ENST00000264231	4	28868

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000401	0.850	125694	0	54	125748	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.226	193	202	0.955	0.0000110	2325
Missense in Polyphen		70	72.097	0.97091		807
Synonymous	-0.457	88	82.7	1.06	0.00000423	783
Loss of Function	1.36	9	14.6	0.617	7.11e-7	160

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000304	0.000297
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000328	0.000325
Middle Eastern	0.000217	0.000217
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Important for the maintenance of cardiac function. Plays a regulatory function in heart rate dynamics mediated, at least in part, through cAMP-binding and, probably, by increasing cell surface expression of the potassium channel KCNK2 and enhancing current density. {ECO:0000250|UniProtKB:Q6JWV8, ECO:0000250|UniProtKB:Q9ES82}.

Recessive Scores

• pRec: 0.0911

Intolerance Scores

• loftool: 0.663
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

• pHI: 0.0951
• hipred: N
• hipred_score: 0.216
• ghis: 0.500

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.134

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Popdc2
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); homeostasis/metabolism phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: popdc2
• Affected structure: cardiac muscle cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: regulation of heart rate;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