Skip to main content

Table 1 Genetic and biochemical findings of validation and discovery cases

From: Improving the diagnosis of cobalamin and related defects by genomic analysis, plus functional and structural assessment of novel variants

Reference

Gene

Allele 1 Nucleotide change (protein effect) HGMD number

Allele 2 Nucleotide change (protein effect) HGMD number

Clinical and biochemical findings

VC1

TCN2 a

c.497_498delTC (p.Leu166Profs*7) CD106933

c.497_498delTC (p.Leu166Profs*7) CD106933

2 m pancytopenia, FTT, metabolic acidosis. Improvement after im OHCbl

↑Hcys (pl): 26 μmol/L; ↑C3: 3.4 μmol/L; ↑MMA (ur): 419 mmol/mol creatn

Propionate uptake (FB) (nmol/10 h/mg prot): Normal

-OHCbl (patient/control): 0.76/0.97

+OHCbl (patient/control): 0.98/0.83

VC2

MTR a

c.1348_1349delTCinsGA (p.Ser450Asp)

c.3008-4A > G (p.?) CS135282

2 m apnea, somnolence, hypotonia, seizures

↑Hcys (pl): 79 μmol/L; MMA (ur) (N)

VC3

MTRR

c.1361C > T (p.Ser454Leu) CM032288

c.1769 + 1G > A (p.Glu560_Arg590del)

MGA, low serum vit B12; ↑Hcys (pl): 90 μmol/L; N MMA (ur)

VC4

MMACHC

c.271dupA (p.Arg91Lysfs*14) CI055013

c.271dupA (p.Arg91Lysfs*14) CI055013

NBS: ↑C3 + C3/C2 in DBS

↑Hcys (pl); ↑MMA (ur) > 1000 mmol/mol creatn

VC5

MMACHC a

c.271dupA (p.Arg91Lysfs*14) CI055013

c.626dupT (p.Thr210Aspfs*35) CI095519

NBS: ↑C3 in DBS

↑Hcys: 159 μmol/L; C3 (pl): 8.2 μmol/L; ↑MMA (ur): 608 mmol/mol creatn

Propionate uptake (FB) (nmol/10 h/mg prot):

-OHCbl (patient/control): 0.23/1.90

+OHCbl (patient/control): 2.3/2.34

VC6

MMADHC a

c.57_64del8 (p.Ser20*) CD082071

c.57_64del8 (p.Ser20*) CD082071

4d hypotonia, metabolic acidosis, hyperammonemia

N Hcys (pl); ↑MMA (ur): 5875 mmol/mol creatn;

Propionate uptake (FB) (nmol/10 h/mg prot):

-OHCbl (patient/control): 0.13/3.31

+OHCbl (patient/control): 2.30/3.37

Mutase (FB):N

VC7

MUT a

c.312delC (p.Trp105Glyfs*75)

c.1846C > T (p.Arg616Cys) CM050688

12 m metabolic acidosis

↑MMA (ur): 8810 mmol/mol creatn

VC8

MMAA a

c.64C > T (p.Arg22Ter) CM042745

c.433C > T (p.Arg145Ter) CM042746

5 m metabolic acidosis. Improvement after im OHCbl

↑MMA (ur)

Propionate uptake (FB) (nmol/10 h/mg prot):

-OHCbl (patient/control): 0.12/1.32

+OHCbl (patient/control): 0.42/2.17

Mutase (FB): N

VC9

MMAB a

c.548A > T (p.His183Leu) CM154654

c.570_572dupCCG (p.Arg191dup) CI154655

NBS: ↑C3 in DBS

↑C3 (pl): 7.7 μmol/L; ↑MMA (ur): 830 mmol/mol creatn

Propionate uptake (FB) (nmol/10 h/mg prot):

-OHCbl (patient/control): 0.63/1.90

+OHCbl (patient/control): 1.19/2.34

Mutase (FB): N

P1

TCN1

c.901G > Tb (p.Asp301Tyr) CM099555

c.901G > Tb (p.Asp301Tyr) CM099555

Adult with neurological symptoms and low serum vit B12. Improvement after im OHCbl

↑N Hcys (pl): 17 μmol/L

P2

TCN1

c.901G > Tb (p.Asp301Tyr) CM099555

c.901G > Tb (p.Asp301Tyr) CM099555

Adult with slight anemia and low serum vit B12.

Improvement after im OHCbl

P3

GIF a

c.389C > G (p.Ser130Ter)

c.389C > G (p.Ser130Ter)

7y, anemia since 15 m; low serum vit B12. Improvement after im OHCbl

↑Hcys (pl): 49 μmol/L

P4

AMN a

c.514-34G > A (p.Thr172fs) CS127867

c.1046C > A (p.Ser349Ter)

2y, megaloblastic anemia with low serum vit B12. Improvement after im OHCbl

↑Hcys (pl): 39.9 μmol/L

P5

MMAA

c.593_596delCTGA (p.Thr198Serfs*6) CD043681

c.593_596delCTGA (p.Thr198Serfs*6) CD043681

↑MMA (ur)

P6

MUT a

c.904G > C (p.Ala302Pro)

c.904G > C (p.Ala302Pro)

NBS: ↑C3 + C3/C2 in DBS

↑MMA (ur): > 1000 mol/mol creatn

Propionate uptake (FB) (nmol/10 h/mg prot) - > (mut0)

-OHCbl (patient/control): 0.18/1.16

+OHCbl (patient/control): 0.11/1.02

P7

MUT a

c.671_678dupAATTTATG (p.Val227Asnfs*16) CI050942

c.607G > A (p.Gly203Arg) CM002067

Neonatal presentation

↑MMA (ur)

P8

MUT

c.313 T > C (p.Trp105Arg) CM900166

c.2150G > T (p.Gly717Val) CM920488

7 m metabolic acidosis, lethargy

↑MMA (ur)

P9

MUT a

c.2026G > A (p.Ala676Thr)

c.2026G > A (p.Ala676Thr)

NBS: ↑C3/C2 in DBS

↑C3 (pl): 2.4 μmol/L; ↑MMA (ur): 772 mmol/mol creatn

Propionate uptake (FB) (nmol/10 h/mg prot) - > (mut-)

-OHCbl (patient/control): 0.25/1.16

+OHCbl (patient/control): 1.16/1.02

P10

MUT a

c.243dupA (p.Pro82Thrfs*2)

c.1084-10A > G (p.?) CS128372

↑MMA (ur)

P11

MUT a

TCN1a

c.454C > T (p.Arg152Ter) CM050671 c.901G > Tb (p.Asp301Tyr) CM099555

?

NBS: ↑C3 in DBS

Low serum vit B12; ↑N MMA (ur): 17–58 mmol/mol creatn

P12

MUT

c.671_678dupAATTTATG (p.Val227Asnfs*16) CI050942

c.671_678dupAATTTATG (p.Val227Asnfs*16) CI050942

Neonatal presentation and fatal outcome

↑MMA (ur)

P13

MUT a

c.1420C > T (p. Arg474Ter) CM050685

c.2026G > A (p.Ala676Thr)

NBS: ↑C3/C2 in DBS

↑C3 (pl): 3.4 μmol/L; ↑MMA (ur): 276 mmol/mol creatn

Propionate uptake (FB) (nmol/10 h/mg prot) - > (mut-)

-OHCbl (patient/control): 0.28/1.33

+OHCbl (patient/control): 1.13/1.57

P14

MMAB a

c.220G > T (p.Glu74Ter)

c.548A > T (p.His183Leu) CM154654

NBS: ↑C3/C2 in DBS

↑C3 (pl): 3.64 μmol/L; ↑MMA (ur): 68 mmol/mol creatn

P15

CD320 a

c.262_264delGAG (p.Glu88del) CD104789

c.142 + 5G > A (p.?)

NBS: ↑C3 + C3/C2 in DBS

↑Hcys (pl): 18.3 μmol/L; N C3 + C4DC (pl); ↑MMA (ur): 25–170 mmol/mol creatn

P16

MMACHC a

c.347 T > C (p.Leu116Pro) CM060067

c.347 T > C (p.Leu116Pro) CM060067

NBS: ↑C3 + C3/C2 in DBS

↑MMA (ur): 2000 mmol/mol creatn

P17

MMACHC a

c.271dupA (p.Arg91Lysfs*14) CI055013

c.271dupA (p.Arg91Lysfs*14) CI055013

4d: hypotonia, weight loss, vomiting, ↑lac

↑Hcys (pl): 214 μmol/L; ↑C3: 6.5 μmol/L + ↑C4DC (pl): 0.25 μmol/L

↑MMA (ur): 1197 mmol/mol creatn

P18

MMACHC

c.271dupA (p.Arg91Lysfs*14) CI055013

c.271dupA (p.Arg91Lysfs*14) CI055013

↑Hcys (pl); ↑MMA (ur)

P19

MMADHC a

c.748C > T (p.Arg250Ter) CM081188

c.748C > T (p.Arg250Ter) CM081188

NBS: ↑C3 + C3/C2 in DBS

↑Hcys (pl): 51 μmol/L; ↑C3 (pl): 4.8 μmol/L; MMA (ur): 290 mmol/mol creatn

P20

MMADHC a

c.748C > T (p.Arg250Ter) CM081188

c.748C > T (p.Arg250Ter) CM081188

NBS: ↑C3 + C3/C2 in DBS

↑Hcys (pl): 59 μmol/L; ↑C3 (pl): 8.5 μmol/L; MMA (ur): 1175 mmol/mol creatn

P21

MTRR

c.1361C > T (p.Ser454Leu) CM032288

c.1361C > T (p. Ser454Leu) CM032288

17 m; anemia, psychomotor delay

↑Hcys (pl): 76 μmol/L

P22

MTRR

c.1361C > T (p.Ser454Leu) CM032288

c.1678_1681delGAGA (p.Glu560Asnfs*42) CD159487

10 m seizures, megaloblastic anemia

↑Hcys (pl): 89 μmol/L

P23

SUCLA2 a

c.976G > C (p.Gly326Arg)

c.935 T > C (p.Ile312Thr)

Hypoglycemia at birth, slight PMD during first years

Asymptomatic at 11y

↑-N C3(pl): 1–2.2 μmol/L + C4DC

↑N Lac, 3-OHProp, MMA 27 mmol/mol creatn, MC (ur)

Normal carboxylases activities (FB)

Propionate uptake (FB) (nmol/10 h/mg prot) - > Normal

-OHCbl (patient/control): 0.71/0.75

+OHCbl (patient/control): 0.79/1.13

P24

ACSF3 a

c.424C > T (p.Gln142Ter)

c.1446_1447delCA (p.Tyr482Ter)

NBS: ↑MMA (ur) since newborn: 512 mmol/mol creatn

Asymptomatic at 3y

P25

ACSF3 a

c.1075G > A (p.Glu359Lys) CM116777

c.1075G > A (p.Glu359Lys) CM116777

5y PMD, bilateral sensorineural hearing loss

AC (pl): N; ↑MMA (ur): 360 mmol/mol creatn

P26

ACSF3 a

c.1075G > A (p.Glu359Lys) CM116777

c.1672C > T (p.Arg558Trp) CM116840

Seizures since first months of age

At 12y seizures + dystonia

AC (pl): N; ↑MMA (ur): 124–560 mmol/mol creatn

Normal propionate uptake ± OHCbl (FB)

P27

ACSF3

c.820C > T (p.Gln274Ter)

c.820C > T (p.Gln274Ter)

NBS: ↑MMA (ur) since newborn. Asymptomatic at 7 m

  1. VC validation case, C3 propionylcarnitine, C2 acetylcarnitine, C4DC methylmalonylcarnitine, DBS dried blood spots, FB fibroblasts, Hcys homocysteine, im intramuscular, MMA methylmalonic acid, OHCbl hydroxocobalamin, ur urine, pl plasma, Lac Lactate, MC methylcitrate, NBS newborn screening, PMD psychomotor delay
  2. aMutations confirmed in parents; b Variant with uncertain clinical significance; new mutations in bold
  3. Mutations named according to GenBank accession number included in Additional file 3: Table S1