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Variant: NM_000527.5(LDLR):c.257_265del (p.Phe86_Arg88del)

CA10584812

251097 (ClinVar)

Gene: LDLR
Condition: hypercholesterolemia, familial
Inheritance Mode: Semidominant inheritance
UUID: e12e806e-0143-429d-8f72-1f9b775df737

HGVS expressions

NM_000527.5:c.257_265del
NM_000527.5(LDLR):c.257_265del (p.Phe86_Arg88del)
NC_000019.10:g.11102730_11102738del
CM000681.2:g.11102730_11102738del
NC_000019.9:g.11213406_11213414del
CM000681.1:g.11213406_11213414del
NC_000019.8:g.11074406_11074414del
NG_009060.1:g.18350_18358del
ENST00000558518.6:c.257_265del
ENST00000252444.9:n.511_519del
ENST00000455727.6:c.257_265del
ENST00000535915.5:c.190+2385_190+2393del
ENST00000545707.5:c.257_265del
ENST00000557933.5:c.257_265del
ENST00000557958.1:n.343_351del
ENST00000558013.5:c.257_265del
ENST00000558518.5:c.257_265del
NM_000527.4:c.257_265del
NM_001195798.1:c.257_265del
NM_001195799.1:c.190+2385_190+2393del
NM_001195800.1:c.257_265del
NM_001195803.1:c.257_265del
NM_001195798.2:c.257_265del
NM_001195799.2:c.190+2385_190+2393del
NM_001195800.2:c.257_265del
NM_001195803.2:c.257_265del

Uncertain Significance

Met criteria codes 4
PP4 PM2 PM4 BP4
Not Met criteria codes 2
PS4 PP3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Familial Hypercholesterolemia VCEP
The NM_000527.5(LDLR):c.257_265del (p.Phe86_Arg88del) variant is classified as Uncertain significance - insufficient evidence for Familial Hypercholesterolemia by applying evidence code PM2, PM4, BP4 and PP4 as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1016/j.gim.2021.09.012). The supporting evidence is as follows: PM2 - This variant is absent from gnomAD (gnomAD v2.1.1). PM4 - Variant meets PM2 and is in frame deletion. BP4 - No REVEL, splicing is needed: A - not on limits. B - not on limits C - There are 2 AG sites nearby: 1- Wild type canonical acceptor: CAATCCTGTCTCTTCTGTAGTGT: 7.07 Wild type cryptic acceptor: CAACCGCTGCATTCCTCAGTTCT: -15.64 Variant cryptic acceptor: CAACCGCTGCATTCCTCAGTGCG: -13.6 cryptic sites have negative scores, so they are not used 2- > Wild type canonical acceptor: CAATCCTGTCTCTTCTGTAGTGT: 7.07 Wild type cryptic acceptor: CTGGAGGTGCGATGGCCAAGTGG: -7.59 Variant cryptic acceptor: TCCTCAGTGCGATGGCCAAGTGG: -4.74 cryptic sites have negative scores, so they are not used There is a GT site nearby: Wild type canonical acceptor: GTCGTAAGT: 9.9 Wild type cryptic acceptor: CAGTTCTGG: -3.44 Variant cryptic acceptor: CAGTGCGAT: -14.44 cryptic sites have negative scores, so they are not used The variant does not affect splicing, so BP4 is met.. PP4 - Variant meets PM2 and is identified in one index case from PMID 11462246.
Met criteria codes
PP4
Variant meets PM2 and is identified in one index case from PMID 11462246
PM2
This variant is absent from gnomAD (gnomAD v2.1.1).
PM4
Variant meets PM2 and is in frame deletion
BP4
No REVEL, splicing is needed: A - not on limits. B - not on limits C - There are 2 AG sites nearby: 1- Wild type canonical acceptor: CAATCCTGTCTCTTCTGTAGTGT: 7.07 Wild type cryptic acceptor: CAACCGCTGCATTCCTCAGTTCT: -15.64 Variant cryptic acceptor: CAACCGCTGCATTCCTCAGTGCG: -13.6 cryptic sites have negative scores, so they are not used 2- > Wild type canonical acceptor: CAATCCTGTCTCTTCTGTAGTGT: 7.07 Wild type cryptic acceptor: CTGGAGGTGCGATGGCCAAGTGG: -7.59 Variant cryptic acceptor: TCCTCAGTGCGATGGCCAAGTGG: -4.74 cryptic sites have negative scores, so they are not used There is a GT site nearby: Wild type canonical acceptor: GTCGTAAGT: 9.9 Wild type cryptic acceptor: CAGTTCTGG: -3.44 Variant cryptic acceptor: CAGTGCGAT: -14.44 cryptic sites have negative scores, so they are not used The variant does not affect splicing, so BP4 is met.
Not Met criteria codes
PS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2022-08-29
Published on: 2022-12-23
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