Case# Kolehmainen_Proband 2

CasePresentingHPOs HP:0001263, HP:0001875, HP:0001135, HP:0011504, HP:0000252, HP:0001290, HP:0001999

CaseNotHPOs

CasePreviousTesting None

CaseMethod1 Sanger sequencing

CaseMethod2

CaseGenotypingMethod Sanger sequencing of COH1

Variant NM_017890.4(VPS13B):c.7051C>T (p.Arg2351Ter)

ClinVar 2820

CAID

gnomAD 0.00003249 in South Asians

VariantEvidence This variant is a nonsense mutation, introducing a termination of the protein product, and is awarded default points. The variant reported is found in gnomAD with a frequency of 0.00003249 in South Asians. It is not reported in Finnish or non-Finnish European populations.

CaseAddInfo This individual is also reported by Fryns et al, who provide the clinical features observed in this individual.

CasePMIDs 8832131

Case# Kolehmainen_Proband 3

CasePresentingHPOs HP:0001263, HP:0001875, HP:0001135, HP:0011504, HP:0000252, HP:0001290, HP:0001999

CaseNotHPOs

CasePreviousTesting None

CaseMethod1 Sanger sequencing

CaseMethod2

CaseGenotypingMethod Sanger sequencing of COH1

Variant1 c.5426_5427dupAG

ClinVar1 56673

gnomAD1: Not found

Variant2 NM_017890.4(VPS13B):c.2074C>T (p.Arg692Ter)

Published as c.2193C>T

ClinVar2 56650

gnomAD2 0.000004063 (African)

VariantEvidence Compound heterozygous individual. Two variants in trans, both truncating. These variants have been reported in heterozygous state in Family 8 described by Seifert et al (PMID: 16648375) and in two different individuals (in heterozygous state) by El Chehadeh et al. (PMID: 20656880).

CaseAddInfo Individual reported in Fryns et al

CasePMIDs 8832131

Case# RQMR10_V-2

Demographics: Female, 20 yrs at report,

CasePresentingHPOs HP:0000729, HP:0001763, HP:0001761, HP:0001956, HP:0000577

CaseNotHPOs

CasePreviousTesting

CaseMethod1

CaseMethod2

CaseGenotypingMethod

Variant NM_017890.4:c.6879delT(p.Phe2293Leufs*24)

ClinVar

CAID CA4824093

gnomAD 0.00003250 (South Asian)

VariantEvidence The proband is homozygous for the variant. This variant introduces a frameshift, resulting in premature protein truncation. The variant was found to cosegregate with disease in the family and was not found in 293 healthy ethnicity-matched controls. It is reported in a heterozygous state at a frequency of 0.00003250 in South Asians in gnomAD.

CaseAddInfo

CasePMIDs

Case#: ATM02_V-3

Demographics: Male, 18 yrs at report

CasePresentingHPOs: HP:0000752, HP:0001581

CaseNotHPOs:

CasePreviousTesting:

CaseMethod1:

CaseMethod2:

CaseGenotypingMethod:

Variant: NM_017890.4:c.6879delT

ClinVar:

CAID: CA4824093

gnomAD:

VariantEvidence: This variant has been reported in two apparently unrelated families of common ethnicity, and therefore likely founder mutation. Hence, the score is reduced from default.

CaseAddInfo:

CasePMIDs:

Family#PresentingHPOs HP:0001263, HP:0010864, HP:0002370, HP:0000664, HP:0000675, HP:0000545, HP:0001763, HP:0008763, HP:0000430, HP:0012471, HP:0000331, HP:0000303, HP:0000662, HP:0000529, HP:0011228

Absent or single-word speech, box-shaped face

FamilyNotHPOs

CountryOrigin Pakistani

Ethnicity

Race

Family#PreviousTesting None

Family#Method1

Family#Method2

Family#GenotypingMethod DNA samples from three affected (V-2, VI-2, VI-3) and two unaffected individuals (V-3, V-4), were genotyped using the Affymetrix Genome-Wide Human SNP 6.0 microarray.

homozygosity-by-descent (HBD) or autozygosity mapping and copy number variation (CNV) analysis was performed using dChip software.

direct Sanger sequencing of VPS13B was performed, based on homozygosity mapping results, for all 62 exons and splice junctions of VPS13B.

Potential candidate variants were further validated in Pakistani population controls through Sanger sequencing.

Affected 2

Unaffected 0

Segregations 1

PublishedLOD No

eLOD 0.6

AddSegregationInfo Pedigree in Figure 1. 5 affected and 3 unaffected individuals clinically determined.

ProbandLabel RQMR10_V-2

Variant NM_017890.4:c.6879delT(p.Phe2293Leufs*24)

ClinVar

CAID CA4824093

gnomAD 0.00003250 (South Asian)

FamilyAddInfo Complete biochemical testing in affected and unaffected. neurological, psychological, ophthalmological, skeletal, behavioral, dental examinations in affecteds. RQMR10_VI-2 underwent fundoscopic examination.

Family#PresentingHPOs HP:0001263, HP:0002342, HP:0002465, HP:0000729, HP:0001290, HP:0002370, HP:0000574, HP:0000426, HP:0000426, HP:0000637, HP:0000675, HP:0000664, HP:0000545, HP:0001763

FamilyNotHPOs

CountryOrigin Pakistan

Ethnicity

Race

Family#PreviousTesting None

Family#Method1

Family#Method2

Family#GenotypingMethod three affected individuals (V-1, V-3, V-5) and four unaffected individuals (IV-7, IV-8, V-4 and V-6) were genotyped using the Illumina HumanOmniExpress BeadChip.

KaryoStudio program from Illumina Inc. was used to exclude cytogenetic abnormalities, and HBD mapping was performed by using the HomozygosityMapper.

whole exome capturing and sequencing in two affected individuals (V-1 and V-5) identified 1bp deletion at c.6879delT. confirmed by Sanger in affecteds and unaffecteds.

Exclusion of LOF variants in other genes per SFARI gene list.

Potential candidate variants were further validated in additional family members, and Pakistani population controls through Sanger sequencing

Affected 3

Unaffected 2

Segregations 2

PublishedLOD No

eLOD 1.45

AddSegregationInfo Unaffected parents and two unaffected siblings genotyped along with the 3 affected individuals.

ProbandLabel ATM02_V-3

Variant NM_017890.4:c.6879delT

ClinVar

CAID CA4824093

gnomAD 0.00003250 (South Asian)

FamilyAddInfo 3 affected brothers clinically evaluated. 1 underwent biochemical testing.

Case#: Yang_Proband 1

Demographics: 2 yr old Male at diagnosis, Chinese

CasePresentingHPOs: HP:0001263, HP:0100840, HP:0000750, HP:0001290, HP:0001347, HP:0002205, HP:0001875

Height: 76 cm, Weight: 11 Kg, OFC: 43 cm, mild oblique palpebral fissure, low tendon hyperreflexia, intermittent neutropenia

CaseNotHPOs:

CasePreviousTesting: None

CaseMethod1: NGS

CaseMethod2: Sanger sequencing

CaseGenotypingMethod: Single-read sequencing of whole genome of patient and his parents, subsequently validated by Sanger sequencing

Variant1: NM_017890.4:c.5086C>T

ClinVar1: 56803

gnomAD: 0.00005805 (East Asian)

Variant2: NM_017890.4:c.6940+1G>T

CAID2: CA183029776

gnomAD: 0.00005821 (East Asian)

VariantEvidence: The individual is a compound heterozygote with the variant, c.5086C>T, inherited from the father and the variant, c.6940+1G>T, inherited from the mother. Both variants are found at a frequency of 0.000058 in East Asians in gnomAD. The c.5086C>T change is a nonsense mutation resulting in premature termination of protein product, while the c.6940+1G>T is a splice donor alteration. The proband is scored default points.

CaseAddInfo:

CasePMIDs:

TissueExpression/Uberon ID: UBERON:0002113, UBERON:0000955, UBERON:0001987, UBERON:0002108, UBERON:0002048

ExpressionEvidence: Northern Blot analysis showed ubiquitous expression of COH1 transcripts in all tissues analyzed.

Relative quantification and PCR-based fragment analysis revealed expression of the splicing variant (NM_152564.3 utilizing exon 28b) in most human tissues. Almost equal expression of both full-length transcript (NM_017890.3 utilizing exon 28) and splice variant was found for fetal and adult brain as well as adult retina.

Where in paper: Results, under "COH1 is differentially spliced in human brain"