Table 1 Clinical and genetic data of a Pakistani family with pyruvate kinase deficiency.
Demographic and clinical information | Genetic findings | ||
|---|---|---|---|
Age | 13 years | Basic variant information | |
Sex | Female | Chromosome location | 1q22 |
Residence | Peshawar | Genomic position | 155264127 |
Ethnicity/language | Pashtun/Pashto | Gene symbol | PKLR |
ABO, Rh blood type | AB, negative | Gene name | Pyruvate kinase L/R |
Hemoglobin (Hb) | 7.6 gm/dL | Ensembl Gene ID | ENSG00000143627 |
Pyruvate kinase (PK) | 12.4 U/g Hb | OMIM ID | 609712 |
Spleen | Palpable, splenomegaly (spleen size 8.8 cm) | Transcript ID | NM_000298.6 |
Liver | Palpable, hepatomegaly | Protein ID | NP_000289.1 |
Temperature (Axillary) | 36.1 °C | Exon number | 7 |
Peripheral pulse rate | 114 | cDNA change | c.1015G > A |
Respiratory rate | 24 br/minute | Protein change | p.Asp339Asn |
Systolic blood pressure | 94 mm Hg | Variant type | SNV |
Diastolic blood pressure | 50 mm Hg | Variant status | Novel |
Oxygen saturation | 0.99 | RS ID | rs747097960 |
Height (third percentile) | 94.3 cm | In silico analysis | |
Weight (third percentile) | 13.4 kg | gnomAD (All) MAF | 0.00001592 |
Body surface area (BSA) | 0.59 m2 | gnomAD (South Asian) MAF | 0.0001307 |
Body mass index (BMI) | 15.1 kg/m2 | gnomAD homozygotes | 0 |
Folic acid | 1 mg, PO, daily, 30 days | ACMG classification | Likely pathogenic |
Transfusion started | 22 days after birth | ClinVar/HGMD | N/A |
Transfusion frequency | Once a month to once every 3 months | DEOGEN2 | Damaging |
Allergies | No known allergies | LRT | Deleterious |
Bone marrow biopsy | Marked erythroid hyperplasia with marked reticulocytosis | MutPred | Pathogenic |
Musculoskeletal | Normal strength | Mutation assessor | Highly damaging |
Lymphatics | No lymphadenopathy | MutationTaster | Disease causing |
Integumentary | No rash | PROVEAN | Damaging |
Neurologic | Alert | PrimateAI | Damaging |
Sodium level | 137 mmol/L | REVEL | Pathogenic |
Potassium level | 4.1 mmol/L | SIFT | Damaging |
Chloride Level | 109 mmol/L | Polyphen-2 | Probably damaging |
CO2 | 22 mmol/L | FATHMM-MKL | Damaging |
AGAP | 6 mmol/L | DANN | 0.9993 |
Miscellaneous | Lack of expected normal physiological development in childhood | CADD PHRED score (GRCh37-v1.6) | 29.5 |
Final diagnosis | Pyruvate kinase deficiency | Evolutionary conservation score (PhyloP100way) | 7.564 |