ClinVar Miner

Submissions for variant NM_019112.4(ABCA7):c.4208del (p.Leu1403fs)

gnomAD frequency: 0.00076  dbSNP: rs538591288
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
CeGaT Center for Human Genetics Tuebingen RCV000415942 SCV000493136 likely pathogenic not provided 2017-08-01 criteria provided, single submitter clinical testing
Invitae RCV000415942 SCV001118077 likely benign not provided 2019-12-31 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003422384 SCV004116493 likely pathogenic ABCA7-related condition 2023-04-21 criteria provided, single submitter clinical testing The ABCA7 c.4208delT variant is predicted to result in a frameshift and premature protein termination (p.Leu1403Argfs*7). Loss of function variants in ABCA7 have been shown to be enriched in patients with Alzheimer’s disease (Le Guennec et al. 2016. PubMed ID: 27037229). This variant has been identified in patients with Alzheimer’s disease and with other non-Alzheimer’s disease neuropathologies (Le Guennec et al. 2016. PubMed ID: 27037229; Allen et al. 2017. PubMed ID: 28097223; Bellenguez et al. 2017. PubMed ID: 28789839; May et al. 2018. PubMed ID: 29577078). This variant has also been identified in control populations (Allen et al. 2017. PubMed ID: 28097223; Bellenguez et a. 2017. PubMed ID: 28789839; May et al. 2018. PubMed ID: 29577078). However, the control populations may have been too young for symptoms to be identified. Of note, one report identified the c.4208del variant in three family members, one was affected and two were children of the patient who were already experiencing occasional memory complications (May et al. 2018. PubMed ID: 29577078). Functional studies have shown that carriers of the c.4208del variant have decreased protein levels (odds ratio 2-4), but unchanged mRNA levels (OMIM #605414; Allen et al. 2017. PubMed ID: 28097223; De Roeck et al. 2017. PubMed ID: 28447221). Pathogenic alterations in the ABCA7 gene may display incomplete penetrance, or at least late-onset complete penetrance. Taken together, this variant is interpreted as likely pathogenic.

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