ClinVar Miner

Variants with conflicting interpretations studied for Disorders of Intracellular Cobalamin Metabolism

Coded as:
Minimum review status of the submission for Disorders of Intracellular Cobalamin Metabolism: Y axis collection method of the submission for Disorders of Intracellular Cobalamin Metabolism:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:
ClinVar version:

If a variant has more than two submissions, it may have multiple conflicts and therefore be counted in more than one conflict column. If this is the case, the "Variants with any kind of conflict" cell will be less than the sum of the conflicted variants cells to its left.

Variants with only 1 submission Variants with at least 2 submissions and no conflicts Variants with a synonymous conflict
(e.g. benign vs non-pathogenic)
Variants with a confidence conflict
(e.g. benign vs likely benign)
Variants with a benign or likely benign vs uncertain conflict Variants with a category conflict
(e.g. benign vs affects)
Variants with a clinically significant conflict
(e.g. benign vs pathogenic)
Variants with any kind of conflict
246 36 0 25 50 2 3 77

Significance breakdown #

In the table below, cells that correspond to a term paired with itself represent synonymous conflicts, i.e. variants that have been annotated with different terms that map to the same standard term. To compare the terms that were actually submitted, check the box in the filters section at the top of this page.

All conditions
Disorders of Intracellular Cobalamin Metabolism pathogenic likely pathogenic uncertain significance likely benign benign drug response risk factor
pathogenic 0 1 1 0 0 0 0
likely pathogenic 1 0 0 0 0 0 0
uncertain significance 2 1 0 35 18 0 0
likely benign 0 0 1 0 23 0 0
benign 0 0 5 0 0 1 2

Condition to condition summary #

Total conditions: 13
Download table as spreadsheet
Condition Variants with only 1 submission Variants with at least 2 submissions and no conflicts Variants with a synonymous conflict
(e.g. benign vs non-pathogenic)
Variants with a confidence conflict
(e.g. benign vs likely benign)
Variants with a benign or likely benign vs uncertain conflict Variants with a category conflict
(e.g. benign vs affects)
Variants with a clinically significant conflict
(e.g. benign vs pathogenic)
Variants with any kind of conflict
not provided 0 5 0 15 34 0 0 49
not specified 0 23 0 21 27 0 0 48
Gastrointestinal stroma tumor 0 0 0 0 5 0 0 5
Homocystinuria-Megaloblastic anemia due to defect in cobalamin metabolism, cblE complementation type 0 2 0 1 1 0 1 3
Methylmalonic acidemia with homocystinuria 0 3 0 1 0 0 2 3
Neural tube defects, folate-sensitive, susceptibility to 0 0 0 0 0 2 0 2
Donnai Barrow syndrome 0 0 0 0 1 0 0 1
Down syndrome, susceptibility to 0 0 0 0 0 1 0 1
Homocystinuria; Decreased methionine synthase activity 0 0 0 1 0 0 0 1
Intellectual disability, profound; Seizure disorder 0 0 0 1 0 0 0 1
METHYLCOBALAMIN DEFICIENCY, cblG TYPE 0 2 0 0 1 0 0 1
METHYLMALONIC ACIDURIA AND HOMOCYSTINURIA, cblF TYPE 0 2 0 1 0 0 0 1
methotrexate response - Toxicity/ADR 0 0 0 0 0 1 0 1

All variants with conflicting interpretations #

Total variants: 77
Download table as spreadsheet
HGVS dbSNP
NM_000254.2(MTR):c.*16del rs67705775
NM_000254.2(MTR):c.1033G>A (p.Val345Ile) rs145006491
NM_000254.2(MTR):c.1076-8C>T rs115186224
NM_000254.2(MTR):c.1080A>G (p.Leu360=) rs141861479
NM_000254.2(MTR):c.1437C>T (p.Asp479=) rs115424814
NM_000254.2(MTR):c.1722T>C (p.Ser574=) rs142857114
NM_000254.2(MTR):c.181A>C (p.Arg61=) rs886046217
NM_000254.2(MTR):c.250-7G>A rs184332230
NM_000254.2(MTR):c.2686C>T (p.Leu896=) rs147762307
NM_000254.2(MTR):c.2756A>G (p.Asp919Gly) rs1805087
NM_000254.2(MTR):c.2815G>C (p.Gly939Arg) rs113042166
NM_000254.2(MTR):c.2994C>T (p.Asn998=) rs778549407
NM_000254.2(MTR):c.3079C>T (p.Arg1027Trp) rs116836001
NM_000254.2(MTR):c.3337G>A (p.Ala1113Thr) rs146071220
NM_000254.2(MTR):c.34+10C>T rs376679817
NM_000254.2(MTR):c.340-6C>T rs7526063
NM_000254.2(MTR):c.3474G>A (p.Leu1158=) rs142113735
NM_000254.2(MTR):c.3477C>T (p.Asp1159=) rs117061132
NM_000254.2(MTR):c.3491G>A (p.Arg1164His) rs61736326
NM_000254.2(MTR):c.3518C>T (p.Pro1173Leu) rs121913578
NM_000254.2(MTR):c.3583A>G (p.Ile1195Val) rs149476106
NM_000254.2(MTR):c.3599-10C>A rs41530146
NM_000254.2(MTR):c.3665A>G (p.Asn1222Ser) rs61739582
NM_000254.2(MTR):c.3712-7T>G rs151081130
NM_000254.2(MTR):c.742G>A (p.Val248Met) rs142648132
NM_000254.2(MTR):c.858C>T (p.Pro286=) rs146019467
NM_000254.2(MTR):c.940G>A (p.Asp314Asn) rs2229274
NM_002454.2(MTRR):c.1678_1681delGAGA (p.Glu560Asnfs) rs768980918
NM_002454.3(MTRR):c.-26+14C>T rs368193742
NM_002454.3(MTRR):c.1049A>G (p.Lys350Arg) rs162036
NM_002454.3(MTRR):c.1091_1093del (p.Cys364del) rs796052001
NM_002454.3(MTRR):c.1155G>A (p.Leu385=) rs2287779
NM_002454.3(MTRR):c.1243C>T (p.Arg415Cys) rs2287780
NM_002454.3(MTRR):c.1349C>G (p.Pro450Arg) rs16879334
NM_002454.3(MTRR):c.1653G>A (p.Pro551=) rs139206262
NM_002454.3(MTRR):c.1761T>C (p.Tyr587=) rs6874544
NM_002454.3(MTRR):c.1783C>T (p.His595Tyr) rs10380
NM_002454.3(MTRR):c.1982A>G (p.His661Arg) rs148909799
NM_002454.3(MTRR):c.210C>G (p.Arg70=) rs41282641
NM_002454.3(MTRR):c.524C>T (p.Ser175Leu) rs1532268
NM_002454.3(MTRR):c.540G>A (p.Val180=) rs149037732
NM_002454.3(MTRR):c.66A>G (p.Ile22Met) rs1801394
NM_002454.3(MTRR):c.739C>T (p.Pro247Ser) rs114053717
NM_002454.3(MTRR):c.769T>A (p.Ser257Thr) rs2303080
NM_002454.3(MTRR):c.869T>C (p.Ile290Thr) rs144899305
NM_002454.3(MTRR):c.876C>T (p.Thr292=) rs144724549
NM_002454.3(MTRR):c.997C>G (p.Leu333Val) rs10064631
NM_015506.2(MMACHC):c.271dupA rs398124292
NM_015506.3(MMACHC):c.178G>C (p.Asp60His) rs6662272
NM_015506.3(MMACHC):c.277-4C>G rs199889403
NM_015506.3(MMACHC):c.326C>T (p.Pro109Leu) rs747214324
NM_015506.3(MMACHC):c.389A>G (p.Tyr130Cys) rs200094982
NM_015506.3(MMACHC):c.433A>T (p.Ile145Leu) rs74365027
NM_015506.3(MMACHC):c.440G>C (p.Gly147Ala) rs140522266
NM_015506.3(MMACHC):c.691T>C (p.Leu231=) rs373198842
NM_015506.3(MMACHC):c.738C>T (p.Pro246=) rs16832550
NM_015506.3(MMACHC):c.766_771del (p.Ala256_Pro257del) rs796064513
NM_015506.3(MMACHC):c.799C>T (p.Arg267Trp) rs34258482
NM_015702.3(MMADHC):c.-16A>G rs144111552
NM_015702.3(MMADHC):c.-49T>C rs79997772
NM_015702.3(MMADHC):c.-60G>A rs886054923
NM_015702.3(MMADHC):c.412G>A (p.Glu138Lys) rs61746421
NM_015702.3(MMADHC):c.428G>T (p.Ser143Ile) rs34886916
NM_015702.3(MMADHC):c.478+6T>G rs13402787
NM_015702.3(MMADHC):c.515A>C (p.Lys172Thr) rs147318949
NM_015702.3(MMADHC):c.578T>C (p.Val193Ala) rs147370143
NM_015702.3(MMADHC):c.617A>G (p.Asn206Ser) rs138607412
NM_015702.3(MMADHC):c.87A>C (p.Lys29Asn) rs61750442
NM_018368.4(LMBRD1):c.-18T>A rs202192515
NM_018368.4(LMBRD1):c.1192T>C (p.Tyr398His) rs185334169
NM_018368.4(LMBRD1):c.18G>C (p.Ala6=) rs149650795
NM_018368.4(LMBRD1):c.384T>C (p.Asp128=) rs143642515
NM_018368.4(LMBRD1):c.801C>T (p.Arg267=) rs34327883
NM_018368.4(LMBRD1):c.897C>T (p.Gly299=) rs757392138
NM_018368.4(LMBRD1):c.980+11T>C rs114726590
NM_018368.4(LMBRD1):c.981-10dup rs202207965
NM_018368.4(LMBRD1):c.981-11A>T rs75847296

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