PRRC2C

proline rich coiled-coil 2C

Basic information

Region (hg38): 1:171485530-171593511

Previous symbols: [ "BAT2D1", "BAT2L2" ]

Links

ENSG00000117523 ∙ NCBI:23215 ∙ OMIM:617373 ∙ HGNC:24903 ∙ Uniprot:Q9Y520 ∙ 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 PRRC2C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRRC2C 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				6		6
missense			163	11		174
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	164	17	0

Variants in PRRC2C

This is a list of pathogenic ClinVar variants found in the PRRC2C region.

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

Position	Type	Phenotype	Significance	ClinVar
1-171512165-A-T		not specified	Uncertain significance (Jun 28, 2022)
1-171513032-C-T			Likely benign (Oct 01, 2024)
1-171513097-A-G		not specified	Uncertain significance (Aug 23, 2021)
1-171514555-G-A		not specified	Uncertain significance (Sep 03, 2024)
1-171515821-A-G		not specified	Uncertain significance (Aug 29, 2024)
1-171515851-G-A		not specified	Uncertain significance (Sep 11, 2024)
1-171517651-A-T		not specified	Uncertain significance (Apr 26, 2024)
1-171517702-A-G		not specified	Uncertain significance (Nov 11, 2024)
1-171517782-G-A		not specified	Uncertain significance (May 28, 2024)
1-171517803-A-G		not specified	Uncertain significance (Apr 12, 2022)
1-171522198-A-T		not specified	Uncertain significance (Sep 27, 2024)
1-171523254-G-C		not specified	Uncertain significance (Feb 21, 2024)
1-171523270-C-T		not specified	Uncertain significance (Sep 24, 2024)
1-171523295-A-T		not specified	Uncertain significance (Apr 13, 2022)
1-171523307-T-G		not specified	Uncertain significance (Nov 25, 2024)
1-171523322-A-G		not specified	Uncertain significance (Feb 27, 2024)
1-171523337-C-T		not specified	Uncertain significance (Sep 10, 2024)
1-171523502-C-G		not specified	Uncertain significance (Jan 31, 2022)
1-171524832-G-A		not specified	Uncertain significance (Feb 13, 2024)
1-171524904-A-G		not specified	Uncertain significance (Aug 09, 2021)
1-171524930-A-G		not specified	Uncertain significance (Aug 02, 2021)
1-171527827-A-G		not specified	Uncertain significance (Feb 27, 2023)
1-171532370-C-T		not specified	Uncertain significance (Apr 22, 2022)
1-171532379-C-A		not specified	Uncertain significance (Apr 18, 2023)
1-171532473-A-G		not specified	Uncertain significance (Dec 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRRC2C	protein_coding	protein_coding	ENST00000338920	33	108000

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	4.47e-16	125570	0	19	125589	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.49	1155	1.42e+3	0.814	0.0000734	18039
Missense in Polyphen		164	269.37	0.60882		3489
Synonymous	-1.00	529	500	1.06	0.0000252	5697
Loss of Function	10.2	10	140	0.0714	0.00000865	1617

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000173	0.000160
Ashkenazi Jewish	0.000205	0.000199
East Asian	0.000109	0.000109
Finnish	0.000185	0.000185
European (Non-Finnish)	0.0000696	0.0000617
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0970

Intolerance Scores

• rvis_EVS: -0.68
• rvis_percentile_EVS: 15.37

Haploinsufficiency Scores

• pHI: 0.759
• hipred: N
• hipred_score: 0.426
• ghis: 0.623

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prrc2c

Gene ontology

• Biological process: hematopoietic progenitor cell differentiation
• Cellular component: cytosol;membrane
• Molecular function: RNA binding;protein C-terminus binding