Case# Patient 3, male, 2yo report, Italy(Compania)

CasePresentingHPOs HP:0001397, HP:0010837, HP:0001976, HP:0002240, HP:0003155, HP:0011967, HP:0001976 (Steatosis, Decreased serum ceruloplasmin, Reduced antithrombin III activity, Hepatomegaly, Elevated alkaline phosphatase, Copper deficiency, Reduced antithrombin III activity)

HPOsFreeText Mild hypertransaminasemia (10mo), slight hepatomegaly, mild speech delay(1.4yo)

CaseNotHPOs n/a

CasePreviousTesting serum metabolic testing: AST 656[nv < 41 U/L], ALT 437[nv < 45 U/L], ALP 1235[nv < 475 U/L], total cholesterol 140[nv < 200 mg/dL], HDL chol 49[nv > 45 mg/dL], LDL chol 96[nv < 160 mg/dL] CK 510 [nv 0-170 U/L], Ceruloplasmin 8 [nv 20-46 mg/dL], Haptoglobin 30[nv 30-250 mg/dL], Copper <40[nv 69-122 μg/dL], type 2 CDG pattern recorded at 1.4yo, retested with similar outcome at 2.4yo

CaseMethod1 Sanger

CaseMethod2 n/a

CaseGenotypingMethod Direct Sanger of TMEM199, no parent testing

Variant (1) NM_152464.2:c.13_14del (p.Leu5AlafsTer30) (2) NM_152464.2(TMEM199):c.92G>C (p.Arg31Pro)

ClinVar (2) 218964

CAID (1) CA8456913

gnomAD (1) 0.00004607(European (Non-Finnish)), 0.00002063(total)-5 heterozygotes (2) 0.00008933(Latino), 0.00004108(Total)-10 heterozygotes

VariantEvidence western blot was not done on this patient's cells, but he has the same TMEM199 variants as the cells that were tested.

CaseAddInfo same variant as "unrelated" family also from Compania, Italy

CasePMIDs 26833330

Family#PresentingHPOs HP:0003124, HP:0003236, HP:0003155, HP:0010837, HP:0001397, HP:0011967, HP:0001405 (High cholesterol, Elevated CK, Elevated alkaline phosphatase, Decreased serum ceruloplasmin, Steatosis, Copper deficiency, Periportal fibrosis)

HPOsFreeText hypertransaminasemia and slight hepatomegaly(2yo), focal steatosis

FamilyNotHPOs n/a

CountryOrigin Italy

Ethnicity n/a

Race n/a

Family#PreviousTesting serum metabolic testing: elevated AST, ALT, ALP, cholesterol(LDL and HDL), and CK, reduced ceruloplasmin and copper, normal haptoglobin. High liver copper, type 2 CDG

Family#Method1 WES

Family#Method2 n/a

Family#GenotypingMethod n/a

Affected 2

Unaffected n/a

Segregations n/a

PublishedLOD n/a

eLOD n/a

AddSegregationInfo n/a

ProbandLabel Patient 1, Female, 2yo onset

Case1PreviousTesting serum metabolic testing: AST 349[nv < 41 U/L], ALT 329[nv < 45 U/L], ALP 1995[nv < 475 U/L], total cholesterol 340[nv < 200 mg/dL], HDL chol 49[nv > 45 mg/dL], LDL chol 256[nv < 160 mg/dL] CK 799 [nv 0-170 U/L], Ceruloplasmin 6 [nv 20-46 mg/dL], Haptoglobin 20[nv 30-250 mg/dL], Copper <40[nv 69-122 μg/dL] recorded at 2yo, retested with similar outcome at 27yo save for restored AST 53U/L and ALT 23U/L

Case2 Patient 2, male, 2yo onset

Case2Previoustesting serum metabolic testing: AST 299[nv < 41 U/L], ALT 221[nv < 45 U/L], ALP 3990[nv < 475 U/L], total cholesterol 240[nv < 200 mg/dL], HDL chol 45[nv > 45 mg/dL], LDL chol 176[nv < 160 mg/dL] CK 442 [nv 0-170 U/L], Ceruloplasmin 4 [nv 20-46 mg/dL], Haptoglobin 40[nv 30-250 mg/dL], Copper <40[nv 69-122 μg/dL] recorded at 2yo. Remained elevated at next check at age 24 save for ALT 50 U/L.

Variant (1) NM_152464.2:c.13_14del (p.Leu5AlafsTer30) (2) NM_152464.2(TMEM199):c.92G>C (p.Arg31Pro)

ClinVar (2) 218964

CAID (1) CA8456913

gnomAD (1) 0.00004607(European (Non-Finnish)), 0.00002063(total)-5 heterozygotes (2) 0.00008933(Latino), 0.00004108(Total)-10 heterozygotes

Variant Evidence No detectable TMEM199 in patient fibroblasts on western blot.

FamilyAddInfo n/a

FamilyPMIDs 26833330

Case# F3-II1, female, 23yo report, Greek

CasePresentingHPOs HP:0008947, HP:0003155, HP:0010837, HP:0003124, HP:0003141, HP:0012347, HP:0012358, HP:0001263 (Infantile Hypotonia, Elevated alkaline phosphatase, Low ceruloplasmin, Elevated cholesterol, Elevated LDL-C, Abnormla N-glycosylation, Abnormal O-glycosylation, Psychomotor delay)

HPOsFreeText Elevated amino transferases

CaseNotHPOs n/a

CasePreviousTesting Serum ALT 36–172 U/l [normal range, 0–50 U/l], AST 31–119 U/l [normal range, 0–50 U/l], ALP 132–1,528 U/l [normal range, < 360 U/l], ceruloplasmin 17–24 mg/dl [normal range, 15–60 mg/dl], cholesterol 231–257 mg/dl [normal range, 120–200 mg/dl], LDL-C 161–171 mg/dl [normal range, 50–130 mg/dl], type 2 CDG

CaseMethod1 Sanger

CaseMethod2 n/a

CaseGenotypingMethod Sanger on patient and parents found variant in heterozygous state in both parents

Variant NM_152464.2(TMEM199):c.92G>C (p.Arg31Pro), homozygous

ClinVar 218964

gnomAD 0.00008933(Latino), 0.00004108(Overall), 10 heterozygotes

VariantEvidence n/a

CaseAddInfo nonconsanguineous

CasePMIDs n/a

Case# F2-II2, male, 41yo report

CasePresentingHPOs HP:0003155, HP:0010837, HP:0003124, HP:0001397, HP:0025321, HP:0003141, HP:0012347, HP:0006579, HP:0000023, HP:0003236 (Elevated alkaline phosphatase, Low ceruloplasmin, Elevated cholesterol, Steatosis, Copper accumulation in liver, Elevated LDL-C, Abnormal N-glycosylation, Neonatal jaundice, Inguinal hernia, Elevated CPK)

HPOsFreeText Inguinal hernia and increased CPK (11yo) minimal fibrosis (30yo), elevated amino transferases (11yo)

CaseNotHPOs HP:0200032 ( Kayser-Fleischer rings)

CasePreviousTesting serum ALT 190 U/l [normal range, 0–50 U/l], AST 153 U/l [normal range, 0–50 U/l], and ALP 718 U/l [normal range, < 360 U/l] (11yo), hepatic dry copper weight of 90 μg/g [normal range, <40 μg/g], ceruloplasmin 8.8 mg/dl [normal range, 15–60 mg/dl], cholesterol 204–337 mg/dl [normal range, 120–200 mg/dl], LDL-C 182–226 mg/dl [normal range, 50–130 mg/dl], type 2 CDG.

19067230: Laboratory tests excluded celiac disease, alpha1-antitrypsin deficiency, cystic fibrosis, galactosaemia and hypobetalipoproteinaemia. Liver iron concentration was normal, normal saturation of transferrin and ferriten, negative for hepatotrophic viruses. Serum anithrombin III (57%, normal range 80–120%) and clotting factor XI (42% , normal range 60–140%) were low.

CaseMethod1 WES

CaseMethod2 n/a

CaseGenotypingMethod WES in patient, sequenced father and mother found to be heterozygous for either variant

Variant NM_152464.2(TMEM199):c.[376-1G>A];[40G>C]

ClinVar 427819

gnomAD n/a for both

VariantEvidence Fig 2C, Western blot: reduced TMEM199 expression in patient fibroblasts

CaseAddInfo nonconsanguineous, father had history of hypercholesterolemia and ischemic heart disease.

CasePMIDs 19067230

Family#PresentingHPOs HP:0003155, HP:0010837, HP:0003124, HP:0001397, HP:0010836, HP:0003141, HP:0012347, HP:0012358, HP:0001976 (Elevated alkaline phosphatase, Low ceruloplasmin, Elevated cholesterol, Steatosis, Abnormality of copper homeostasis, Elevated LDL-C, Abnormal N-glycosylation, Abnormal O-glycosylation, Reduced antithrombin III activity)

HPOsFreeText Elevated amino transferases, minimal fibrosis, slightly decreased coagulation factors XI, XIII, and antithrombin-III

FamilyNotHPOs HP:0200032 (Kayser-Fleischer rings)

CountryOrigin n/a

Ethnicity Greek

Race n/a

Family#PreviousTesting Metabolic work up and anyalysis of coagulation factors, the latter of which showed decreased antithrombin-II, factor XI, factor XIII, and protein S, type 2 CDG. No mutations found in ATP7B, Wilson's disease excluded.

Family#Method1 WES

Family#Method2 Sanger

Family#GenotypingMethod WES on siblings, confirmed heterozygous in parents with Sanger

Affected 2

Unaffected 2

Segregations n/a

PublishedLOD n/a

eLOD n/a

AddSegregationInfo consanguineous

ProbandLabel F1-II2, male, 14yo report

Case1PreviousTesting Serum ALT 54 U/l [normal range, 0–50 U/l], AST 73 U/l [normal range, 0–50 U/l], ALP 745 U/l [normal range, < 360 U/l], ceruloplasmin 11.5 mg/dl [normal range, 15–60 mg/dl], urine copper/creatine ratio 86.9 μg/g [normal range, < 60 μg/g], cholesterol 253 mg/dl [normal range, 120–200 mg/dl], LDL cholesterol 188 mg/dl [normal range, 50–130 mg/dl]

Case2 F1-II3, male, 6yo report

Case2PreviousTesting ALT 210 U/l [normal range, 0–50 U/l], AST 246 U/l [normal range, 0–50 U/l], ALP 1162 U/l [normal range, < 360 U/l], ceruloplasmin 15.6 mg/dl [normal range, 15–60 mg/dl], urine copper/creatine ratio 72.8 μg/g [normal range, < 60 μg/g], cholesterol 336 mg/dl [normal range, 120–200 mg/dl], LDL cholesterol 277 mg/dl [normal range, 50–130 mg/dl]

Variant NM_152464.2(TMEM199):c.20C>A (p.Ala7Glu), homozygous

ClinVar 218965

gnomAD 23 total heterozygotes (sampled from ~242458) for missense changes at this locus, no entry for this particular variant

Variant Evidence Fig 2C, Western blot: reduced TMEM199 expression in patient fibroblasts

FamilyAddInfo n/a

FamilyPMIDs n/a