Table 2 Details of the variants detected in the participants.

From: Molecular characterization of recessively inherited ataxic and neuropathic disorders in consanguineous Pakistani families

Family

Gene

*Position (hg19)

Transcript, cDNA change and Effect

gnomAD AF

ACMG classification, OMIM, Predictions

Comments

RDFA05

MFSD8

Chr4:128851901

NM_152778.3,

c.935T > C,

p.Ile312Thr, missense

0.0000238

VUS

OMIM#611,124

REVEL 0.4 FATHMM 0.32

Segregated with the phenotype.

ClinVar VCV000211495.11

PMID: 39108,195

RDFA09

AFG3L2

Chr18:12337348

NM_006796.2,

c.2167G > A, p.Val723Met, missense

0.0001749

VUS

OMIM#604,581

REVEL 0.58 FATHMM − 2.04

Segregated with the phenotype

ClinVar VCV000214062.16,

PMID: 31111429

RDFA11

SETX

Chr9:135202351

NM_015046.7 c.4633_4636delAGTG, p.Ser1545AlafsTer25,

frameshift

0

OMIM#608,465

FATHMM N/A

Segregated with the phenotype

PMID: 19744353

RDFA07

EHHADH

Chr3:184911093

NM_001966.4,

c.1093T > G,

p.Leu365Val, missense

0.0006347

VUS

OMIM#607,037

REVEL 0.15

FATHMM − 1.2

Segregated with the phenotype, but the dominant disorder Fanconi renotubular syndrome 3 (OMIM# 615605) does not correspond to the observed phenotype of our patients. The amino acid is not conserved in evolution and the variant is predicted to be benign by various software.

RDFA08

(V:7)

ALS2

Chr2:202588157

NM_020919.4

c. 3520 A > T,

p.Lys1174Ter,

nonsense

0.000004008

P,

OMIM#607,225

REVEL N/A

FATHMM N/A

Known pathogenic variant which was only detected in one patient and was absent in his two affected cousins ClinVar VCV000645923.10

PMID: 28600779

RDFA03

GDAP1

Chr8:75276365

NM_018972.3,

c.840delC,

p.Tyr280Ter, nonsense

0

LP

OMIM#606,598

REVEL N/A

FATHMM N/A

Segregated with the phenotype

ClinVar VCV000637127.3

PMID: 25231362

RDFA03

(only homozygous in proband V:1)

MMACHC

Chr1:45973954

NM_001330540.2

c.176T > C, p.Leu59Pro, missense

0.00004811

P

OMIM#277,400

REVEL 0.98

FATH.MM -4.6

Known pathogenic variant of MMACHC. It was only present in the proband (V:1) while absent in all other affected individuals.

ClinVar

VCV000001422.13

PMID: 16311595

RDFA04

GDAP1

Chr8:75272408

NM_018972.3,

c.347T > G,

p.Met116Arg, missense

0.000008122

P

OMIM#606,598

REVEL 0.56

FATHMM − 5.24

Segregated with the phenotype

ClinVar VCV000038411.49

PMID: 15377708

  1. *Human Genome reference GRCh37, ACMG = American college of medical genetics and genomics, OMIM = Online Mendelian inheritance in man REVEL = Rare exome variant ensemble learner, (Higher scores are more deleterious), FATHMM= Functional analysis through hidden Markov models, Lower scores are more deleterious, P= Pathogenic, LP= Likely pathogenic, VUS=Variant of unknown significance, N/A Not applicable or not available.
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