PVALB

parvalbumin, the group of EF-hand domain containing

Basic information

Region (hg38): 22:36800683-36819479

Links

ENSG00000100362 ∙ NCBI:5816 ∙ OMIM:168890 ∙ HGNC:9704 ∙ Uniprot:P20472 ∙ 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 PVALB gene.

• not provided (4 variants)
• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PVALB 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			3		2	5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	3	0	3

Variants in PVALB

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

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

Position	Type	Phenotype	Significance	ClinVar
22-36813664-C-T		not specified	Uncertain significance (Jan 06, 2023)
22-36813741-C-G		not specified	Uncertain significance (Oct 03, 2022)
22-36815104-C-T			Benign (Jun 26, 2018)
22-36815119-C-T		not specified	Uncertain significance (Dec 14, 2023)
22-36815175-G-A			Benign (Jun 26, 2018)
22-36815230-C-T			Uncertain significance (Jan 16, 2020)
22-36815245-G-T			Benign (Jun 26, 2018)
22-36816953-G-T		not specified	Uncertain significance (Feb 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PVALB	protein_coding	protein_coding	ENST00000216200	4	18796

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0866	0.773	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0360	61	61.8	0.987	0.00000308	743
Missense in Polyphen		24	25.809	0.9299		306
Synonymous	0.424	23	25.7	0.894	0.00000160	192
Loss of Function	1.10	2	4.52	0.443	1.89e-7	63

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000355	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: In muscle, parvalbumin is thought to be involved in relaxation after contraction. It binds two calcium ions.

Recessive Scores

• pRec: 0.363

Intolerance Scores

• loftool: 0.556
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.06

Haploinsufficiency Scores

• pHI: 0.401
• hipred: N
• hipred_score: 0.264
• ghis: 0.484

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.164

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pvalb
• Phenotype: cellular phenotype; muscle phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of cytosolic calcium ion concentration
• Cellular component: nucleus;cytoplasm;axon;protein-containing complex;neuronal cell body
• Molecular function: calcium ion binding;protein homodimerization activity;protein heterodimerization activity