We discovered the same microdeletion 2q11.1q11.2 for a fetus presenting with cleft lip/ cardiac malformation/ clinodactyly. It is inherited from a father no yet seen in consultation. Is this variant can be considered as a putative cause of a syndrome with malformations and ID.
Conference Paper Microdeletion 2q11.1q11.2 including haploinsufficiency of SN...
You could try checking at ClinGen:
http://www.ncbi.nlm.nih.gov/projects/dbvar/clingen/
I assume that you already looked at the databasaes (e.g. DESIPHER) and came up empty. Then, get the transmitting father's phenotype. If the father has the same or very similar features there is a reasonable chance that this is causal. In that case, look further in the family for any history suggesting dominant inheritantce. In dominant pedigrees, it does not take too many affected to get a LOD of 3, the definitive proof.
If no onr in the father'd family is unaffected, it could be irrelevant or a "susceptibility factor" requiring additional genetic or envirnomental input. In that case, you are dealing with a complex trait and you will need anywhere from dozens to thousands (depending on the strength of the effect) of similarly affected probands to prove it. Discouraging, I know, but such are the limitations of human knowledge.
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