ClinVar Miner

Variants with conflicting interpretations studied for PKHD1-related disorder

Minimum review status of the submission for PKHD1-related disorder: Collection method of the submission for PKHD1-related disorder:
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 per condition Variants with at least 2 submissions on the same condition 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 conflict
222 120 0 29 87 1 18 125

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
PKHD1-related disorder pathogenic likely pathogenic uncertain significance likely benign benign protective
pathogenic 0 11 5 0 0 1
likely pathogenic 8 0 10 0 0 0
uncertain significance 1 3 0 1 0 0
likely benign 0 0 83 0 5 0
benign 0 0 3 5 0 0

Condition to condition summary #

Total conditions: 4
Download table as spreadsheet
Condition Variants with only 1 submission per condition Variants with at least 2 submissions on the same condition 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 conflict
not provided 0 107 0 25 85 0 15 120
not specified 0 33 0 5 12 0 6 22
Colorectal cancer, protection against 0 0 0 0 0 1 0 1
See cases 0 2 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 125
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_138694.4(PKHD1):c.1964+17G>T rs201349527 0.00517
NM_138694.4(PKHD1):c.9866G>T (p.Ser3289Ile) rs148932323 0.00287
NM_138694.4(PKHD1):c.9788T>C (p.Val3263Ala) rs146519878 0.00261
NM_138694.4(PKHD1):c.1950G>A (p.Arg650=) rs143226202 0.00243
NM_138694.4(PKHD1):c.8345G>C (p.Gly2782Ala) rs147222255 0.00223
NM_138694.4(PKHD1):c.652G>A (p.Glu218Lys) rs149522482 0.00198
NM_138694.4(PKHD1):c.1342G>C (p.Gly448Arg) rs149781976 0.00146
NM_138694.4(PKHD1):c.7307C>T (p.Thr2436Ile) rs147851214 0.00145
NM_138694.4(PKHD1):c.11338C>T (p.Pro3780Ser) rs41273722 0.00140
NM_138694.4(PKHD1):c.6854G>A (p.Gly2285Glu) rs142526715 0.00137
NM_138694.4(PKHD1):c.281+3A>G rs79803080 0.00105
NM_138694.4(PKHD1):c.9215C>T (p.Ala3072Val) rs139306706 0.00104
NM_138694.4(PKHD1):c.275G>A (p.Arg92Gln) rs145886657 0.00101
NM_138694.4(PKHD1):c.11002G>T (p.Asp3668Tyr) rs114237522 0.00095
NM_138694.4(PKHD1):c.1307C>G (p.Thr436Ser) rs146789444 0.00093
NM_138694.4(PKHD1):c.3834C>T (p.Phe1278=) rs145960781 0.00088
NM_138694.4(PKHD1):c.7912-5T>G rs371510537 0.00075
NM_138694.4(PKHD1):c.1925C>T (p.Thr642Ile) rs138968608 0.00070
NM_138694.4(PKHD1):c.7675G>C (p.Val2559Leu) rs150046042 0.00070
NM_138694.4(PKHD1):c.9553G>A (p.Val3185Ile) rs145651593 0.00066
NM_138694.4(PKHD1):c.7744C>T (p.Pro2582Ser) rs200204857 0.00061
NM_138694.4(PKHD1):c.2194G>T (p.Val732Phe) rs201432731 0.00058
NM_138694.4(PKHD1):c.11800G>A (p.Val3934Ile) rs149111536 0.00057
NM_138694.4(PKHD1):c.10210A>G (p.Ile3404Val) rs147612089 0.00056
NM_138694.4(PKHD1):c.2243C>T (p.Ala748Val) rs141622697 0.00056
NM_138694.4(PKHD1):c.3627G>A (p.Leu1209=) rs182216709 0.00056
NM_138694.4(PKHD1):c.10859G>A (p.Arg3620His) rs149163661 0.00054
NM_138694.4(PKHD1):c.5134G>A (p.Gly1712Arg) rs141103838 0.00054
NM_138694.4(PKHD1):c.4871G>A (p.Arg1624Gln) rs190396031 0.00051
NM_138694.4(PKHD1):c.7091T>A (p.Ile2364Asn) rs76260483 0.00050
NM_138694.4(PKHD1):c.107C>T (p.Thr36Met) rs137852944 0.00048
NM_138694.4(PKHD1):c.6782A>G (p.Asn2261Ser) rs146102132 0.00045
NM_138694.4(PKHD1):c.12198C>T (p.His4066=) rs147051900 0.00039
NM_138694.4(PKHD1):c.4266G>A (p.Arg1422=) rs146468152 0.00029
NM_138694.4(PKHD1):c.5235C>T (p.Phe1745=) rs187667255 0.00028
NM_138694.4(PKHD1):c.9493G>A (p.Val3165Met) rs199621305 0.00025
NM_138694.4(PKHD1):c.3303A>G (p.Thr1101=) rs148335285 0.00024
NM_138694.4(PKHD1):c.8554+3A>G rs370312392 0.00021
NM_138694.4(PKHD1):c.7170T>C (p.Thr2390=) rs368101035 0.00020
NM_138694.4(PKHD1):c.9478C>T (p.His3160Tyr) rs147351244 0.00020
NM_138694.4(PKHD1):c.3761C>G (p.Ala1254Gly) rs148901752 0.00019
NM_138694.4(PKHD1):c.2781A>G (p.Gln927=) rs200511208 0.00017
NM_138694.4(PKHD1):c.5534A>G (p.Gln1845Arg) rs566044331 0.00017
NM_138694.4(PKHD1):c.7533A>G (p.Ser2511=) rs200679577 0.00017
NM_138694.4(PKHD1):c.8187C>A (p.Ala2729=) rs149310653 0.00016
NM_138694.4(PKHD1):c.4854C>T (p.Ile1618=) rs140674740 0.00015
NM_138694.4(PKHD1):c.977-7C>G rs1054774956 0.00014
NM_138694.4(PKHD1):c.2637G>A (p.Thr879=) rs147915980 0.00013
NM_138694.4(PKHD1):c.831C>T (p.Ile277=) rs142678486 0.00013
NM_138694.4(PKHD1):c.9663G>A (p.Pro3221=) rs371508721 0.00013
NM_138694.4(PKHD1):c.5829C>T (p.Gly1943=) rs376709130 0.00012
NM_138694.4(PKHD1):c.1974C>T (p.Phe658=) rs199635188 0.00011
NM_138694.4(PKHD1):c.8407T>C (p.Cys2803Arg) rs398124495 0.00011
NM_138694.4(PKHD1):c.1849T>C (p.Tyr617His) rs141177165 0.00010
NM_138694.4(PKHD1):c.6687T>C (p.Ser2229=) rs148497044 0.00010
NM_138694.4(PKHD1):c.6741C>G (p.Cys2247Trp) rs750190287 0.00010
NM_138694.4(PKHD1):c.2162C>T (p.Thr721Met) rs140608845 0.00009
NM_138694.4(PKHD1):c.282-3C>T rs535210707 0.00009
NM_138694.4(PKHD1):c.5193G>A (p.Val1731=) rs146531432 0.00009
NM_138694.4(PKHD1):c.5498C>T (p.Ser1833Leu) rs201105958 0.00009
NM_138694.4(PKHD1):c.8364C>T (p.Thr2788=) rs777017196 0.00009
NM_138694.4(PKHD1):c.9345A>G (p.Glu3115=) rs760710708 0.00009
NM_138694.4(PKHD1):c.11836T>C (p.Leu3946=) rs35403035 0.00008
NM_138694.4(PKHD1):c.1833A>C (p.Thr611=) rs142922408 0.00008
NM_138694.4(PKHD1):c.4866C>A (p.Leu1622=) rs571966529 0.00008
NM_138694.4(PKHD1):c.5520C>T (p.Cys1840=) rs535128714 0.00008
NM_138694.4(PKHD1):c.708-5C>T rs371844893 0.00008
NM_138694.4(PKHD1):c.880+5C>T rs759601015 0.00008
NM_138694.4(PKHD1):c.1816C>T (p.Arg606Trp) rs560133266 0.00006
NM_138694.4(PKHD1):c.2091G>A (p.Thr697=) rs147826962 0.00006
NM_138694.4(PKHD1):c.3628+9C>A rs552339299 0.00006
NM_138694.4(PKHD1):c.4870C>T (p.Arg1624Trp) rs200391019 0.00006
NM_138694.4(PKHD1):c.5912G>A (p.Gly1971Asp) rs180675584 0.00006
NM_138694.4(PKHD1):c.8518C>T (p.Arg2840Cys) rs200432861 0.00006
NM_138694.4(PKHD1):c.9576C>T (p.Ser3192=) rs201670044 0.00006
NM_138694.4(PKHD1):c.11607C>T (p.Ala3869=) rs752509045 0.00005
NM_138694.4(PKHD1):c.9530T>C (p.Ile3177Thr) rs200511261 0.00005
NM_138694.4(PKHD1):c.624T>C (p.His208=) rs767511678 0.00004
NM_138694.4(PKHD1):c.666C>T (p.Ile222=) rs538867151 0.00004
NM_138694.4(PKHD1):c.1123C>T (p.Arg375Trp) rs376040501 0.00003
NM_138694.4(PKHD1):c.1913T>C (p.Met638Thr) rs181546197 0.00003
NM_138694.4(PKHD1):c.2507T>C (p.Val836Ala) rs199568593 0.00003
NM_138694.4(PKHD1):c.11747C>G (p.Ser3916Ter) rs760426769 0.00002
NM_138694.4(PKHD1):c.2265G>A (p.Pro755=) rs375603741 0.00002
NM_138694.4(PKHD1):c.6490+4G>A rs764221265 0.00002
NM_138694.4(PKHD1):c.668-3C>T rs775002568 0.00002
NM_138694.4(PKHD1):c.778+10C>G rs1365502451 0.00002
NM_138694.4(PKHD1):c.8425G>A (p.Gly2809Arg) rs398124497 0.00002
NM_138694.4(PKHD1):c.873C>T (p.Thr291=) rs769773725 0.00002
NM_138694.4(PKHD1):c.2697T>A (p.Thr899=) rs1562217633 0.00001
NM_138694.4(PKHD1):c.2864T>G (p.Phe955Cys) rs777158800 0.00001
NM_138694.4(PKHD1):c.3747T>G (p.Cys1249Trp) rs748540413 0.00001
NM_138694.4(PKHD1):c.4292G>A (p.Cys1431Tyr) rs753307105 0.00001
NM_138694.4(PKHD1):c.5221G>A (p.Val1741Met) rs137852946 0.00001
NM_138694.4(PKHD1):c.6042C>T (p.Tyr2014=) rs373208457 0.00001
NM_138694.4(PKHD1):c.642G>A (p.Gln214=) rs762584715 0.00001
NM_138694.4(PKHD1):c.7308T>G (p.Thr2436=) rs771622189 0.00001
NM_138694.4(PKHD1):c.7641A>G (p.Ser2547=) rs771563591 0.00001
NM_138694.4(PKHD1):c.8068T>C (p.Trp2690Arg) rs886061616 0.00001
NM_138694.4(PKHD1):c.8317G>T (p.Val2773Leu) rs747322128 0.00001
NM_138694.4(PKHD1):c.8997A>G (p.Pro2999=) rs777095602 0.00001
NM_138694.4(PKHD1):c.9308G>A (p.Gly3103Asp) rs753264751 0.00001
NM_138694.4(PKHD1):c.9461A>G (p.Asp3154Gly) rs1477456222 0.00001
NM_138694.4(PKHD1):c.9619G>A (p.Ala3207Thr) rs1242089464 0.00001
NM_138694.4(PKHD1):c.10411G>A (p.Val3471Ile) rs553752644
NM_138694.4(PKHD1):c.10893T>C (p.Tyr3631=) rs1290859259
NM_138694.4(PKHD1):c.12147G>A (p.Glu4049=) rs1561967407
NM_138694.4(PKHD1):c.158A>G (p.Asn53Ser) rs141790557
NM_138694.4(PKHD1):c.2264C>T (p.Pro755Leu) rs1057517158
NM_138694.4(PKHD1):c.2269A>C (p.Ile757Leu) rs777183511
NM_138694.4(PKHD1):c.274C>T (p.Arg92Trp) rs370277502
NM_138694.4(PKHD1):c.3122G>A (p.Gly1041Asp) rs794727466
NM_138694.4(PKHD1):c.3940del (p.Ser1314fs) rs1057517273
NM_138694.4(PKHD1):c.449-15TTC[2] rs545812620
NM_138694.4(PKHD1):c.4844C>T (p.Thr1615Met) rs147529495
NM_138694.4(PKHD1):c.5133C>T (p.Ala1711=) rs144841026
NM_138694.4(PKHD1):c.528-17dup rs753686281
NM_138694.4(PKHD1):c.5909-2del rs1334913120
NM_138694.4(PKHD1):c.6866-2_6866-1delinsGA rs1562581286
NM_138694.4(PKHD1):c.7264T>G (p.Cys2422Gly) rs201881567
NM_138694.4(PKHD1):c.847T>C (p.Phe283Leu) rs375145340
NM_138694.4(PKHD1):c.85G>T (p.Glu29Ter) rs398124498
NM_138694.4(PKHD1):c.9369G>T (p.Ala3123=) rs745523374
NM_138694.4(PKHD1):c.9719G>T (p.Arg3240Leu) rs146649803
NM_138694.4(PKHD1):c.9727del (p.Ile3243fs) rs1562221540

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